Starting phenix.real_space_refine on Mon Feb 19 09:27:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/02_2024/8hh9_34756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/02_2024/8hh9_34756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/02_2024/8hh9_34756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/02_2024/8hh9_34756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/02_2024/8hh9_34756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/02_2024/8hh9_34756_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 415": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 415": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 127": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 383": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 415": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E ARG 352": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E ARG 405": "NH1" <-> "NH2" Residue "E ARG 435": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 120": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "F ARG 333": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 368": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F ARG 405": "NH1" <-> "NH2" Residue "F ARG 435": "NH1" <-> "NH2" Residue "F ARG 454": "NH1" <-> "NH2" Residue "F ARG 458": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G ARG 10": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 200": "NH1" <-> "NH2" Residue "G ARG 240": "NH1" <-> "NH2" Residue "G ARG 256": "NH1" <-> "NH2" Residue "G ARG 264": "NH1" <-> "NH2" Residue "G ARG 266": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24250 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.61, per 1000 atoms: 0.52 Number of scatterers: 24250 At special positions: 0 Unit cell: (129.36, 122.32, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.91 Conformation dependent library (CDL) restraints added in 4.6 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 22 sheets defined 42.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.653A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.708A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 394 removed outlier: 3.983A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.298A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'B' and resid 151 through 156 removed outlier: 4.167A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.507A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.742A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.260A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 373 through 395 removed outlier: 4.038A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.905A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.571A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.582A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.798A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.179A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 397 removed outlier: 3.533A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 removed outlier: 4.036A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.658A pdb=" N ILE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 3.831A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.687A pdb=" N ALA C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 164 through 178 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 242 removed outlier: 5.226A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.584A pdb=" N SER D 265 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 3.738A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 386 removed outlier: 3.893A pdb=" N TYR D 377 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 409 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 No H-bonds generated for 'chain 'D' and resid 450 through 453' Processing helix chain 'D' and resid 459 through 470 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 5.274A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.563A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 291 removed outlier: 4.542A pdb=" N ALA E 282 " --> pdb=" O PRO E 279 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU E 290 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 291 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 3.505A pdb=" N GLU E 379 " --> pdb=" O GLN E 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.910A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.986A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 removed outlier: 3.624A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 453' Processing helix chain 'E' and resid 459 through 468 removed outlier: 3.747A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.470A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 242 removed outlier: 5.316A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 265 Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.572A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.748A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 387 removed outlier: 4.579A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.830A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 468 removed outlier: 3.579A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 56 removed outlier: 3.521A pdb=" N ARG G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 4.155A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.619A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 removed outlier: 4.005A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 209 through 283 Proline residue: G 218 - end of helix removed outlier: 3.714A pdb=" N ALA G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.794A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.938A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.434A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.562A pdb=" N ILE A 167 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A 342 " --> pdb=" O ILE A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.558A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.517A pdb=" N ARG B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 166 through 169 Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.600A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.491A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.053A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.910A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.481A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.568A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 188 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.475A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 211 through 217 removed outlier: 6.979A pdb=" N SER E 183 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL E 184 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU E 248 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA E 186 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE E 250 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 188 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER E 299 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU E 249 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 301 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE E 251 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE E 303 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY E 155 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR E 328 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE E 157 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN E 330 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 4 through 10 removed outlier: 6.647A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.799A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ASP F 252 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA F 186 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 182 through 187 removed outlier: 3.541A pdb=" N MET G 170 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP G 136 " --> pdb=" O VAL G 117 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2604 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: 8.10 Time building geometry restraints manager: 10.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7260 1.33 - 1.45: 3280 1.45 - 1.57: 13939 1.57 - 1.69: 22 1.69 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N GLY D 159 " pdb=" CA GLY D 159 " ideal model delta sigma weight residual 1.449 1.495 -0.046 1.45e-02 4.76e+03 1.01e+01 bond pdb=" N ALA D 160 " pdb=" CA ALA D 160 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.33e-02 5.65e+03 8.92e+00 bond pdb=" CZ ARG E 454 " pdb=" NH2 ARG E 454 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.62e+00 bond pdb=" CZ ARG E 404 " pdb=" NH2 ARG E 404 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.17e+00 bond pdb=" N THR E 192 " pdb=" CA THR E 192 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.33e-02 5.65e+03 6.96e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 99.42 - 107.49: 915 107.49 - 115.56: 15259 115.56 - 123.63: 16718 123.63 - 131.70: 527 131.70 - 139.77: 14 Bond angle restraints: 33433 Sorted by residual: angle pdb=" O GLY D 158 " pdb=" C GLY D 158 " pdb=" N GLY D 159 " ideal model delta sigma weight residual 122.70 113.47 9.23 1.30e+00 5.92e-01 5.04e+01 angle pdb=" C ASP E 252 " pdb=" CA ASP E 252 " pdb=" CB ASP E 252 " ideal model delta sigma weight residual 110.90 102.86 8.04 1.58e+00 4.01e-01 2.59e+01 angle pdb=" OE1 GLN E 412 " pdb=" CD GLN E 412 " pdb=" NE2 GLN E 412 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA ASP E 252 " pdb=" C ASP E 252 " pdb=" O ASP E 252 " ideal model delta sigma weight residual 120.70 116.25 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" OD1 ASN E 413 " pdb=" CG ASN E 413 " pdb=" ND2 ASN E 413 " ideal model delta sigma weight residual 122.60 118.32 4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 14181 22.71 - 45.41: 741 45.41 - 68.11: 100 68.11 - 90.82: 36 90.82 - 113.52: 1 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 53.53 -113.52 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" CA LYS D 334 " pdb=" C LYS D 334 " pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR E 341 " pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta harmonic sigma weight residual 0.00 23.60 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3284 0.064 - 0.128: 543 0.128 - 0.193: 21 0.193 - 0.257: 3 0.257 - 0.321: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA ALA E 343 " pdb=" N ALA E 343 " pdb=" C ALA E 343 " pdb=" CB ALA E 343 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PRO E 342 " pdb=" N PRO E 342 " pdb=" C PRO E 342 " pdb=" CB PRO E 342 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL D 162 " pdb=" CA VAL D 162 " pdb=" CG1 VAL D 162 " pdb=" CG2 VAL D 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 341 " -0.088 2.00e-02 2.50e+03 5.16e-02 5.32e+01 pdb=" CG TYR E 341 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 341 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 341 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 341 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR E 341 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR E 341 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR E 341 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 414 " 0.079 2.00e-02 2.50e+03 5.12e-02 4.58e+01 pdb=" CG PHE E 414 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE E 414 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE E 414 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 PHE E 414 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 414 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 414 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 377 " 0.078 2.00e-02 2.50e+03 3.96e-02 3.14e+01 pdb=" CG TYR E 377 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 377 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 377 " 0.044 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 16194 3.06 - 3.67: 36520 3.67 - 4.29: 53541 4.29 - 4.90: 90610 Nonbonded interactions: 196966 Sorted by model distance: nonbonded pdb=" OE2 GLU E 190 " pdb=" CE1 PHE E 215 " model vdw 1.830 3.340 nonbonded pdb=" CB ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.920 3.460 nonbonded pdb=" CA ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.929 3.470 nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 2.006 2.170 ... (remaining 196961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 11.130 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 64.720 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.120 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.004 0.048 24655 Z= 0.264 Angle : 0.667 10.757 33433 Z= 0.388 Chirality : 0.046 0.321 3852 Planarity : 0.005 0.052 4362 Dihedral : 13.989 113.525 9347 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 0.43 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3115 helix: 1.09 (0.15), residues: 1249 sheet: 0.67 (0.24), residues: 505 loop : -0.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 470 PHE 0.079 0.002 PHE E 414 TYR 0.088 0.002 TYR E 341 ARG 0.009 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 3.006 Fit side-chains REVERT: B 62 MET cc_start: 0.8191 (tpt) cc_final: 0.7708 (tpt) REVERT: B 455 ARG cc_start: 0.8911 (ttp80) cc_final: 0.8545 (ttp80) REVERT: D 164 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: D 378 LYS cc_start: 0.6753 (mmtp) cc_final: 0.6490 (ptmt) REVERT: D 389 MET cc_start: 0.6715 (ttt) cc_final: 0.6020 (tmm) REVERT: D 462 VAL cc_start: 0.4425 (t) cc_final: 0.4221 (t) REVERT: G 67 MET cc_start: 0.7535 (mmm) cc_final: 0.7119 (mmp) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.3372 time to fit residues: 76.2577 Evaluate side-chains 107 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain E residue 251 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 0.0270 chunk 281 optimal weight: 0.9980 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN D 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24655 Z= 0.286 Angle : 0.564 10.051 33433 Z= 0.290 Chirality : 0.045 0.155 3852 Planarity : 0.004 0.048 4362 Dihedral : 8.202 115.871 3553 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.43 % Allowed : 5.76 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3115 helix: 1.10 (0.15), residues: 1254 sheet: 0.66 (0.24), residues: 504 loop : -0.14 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 470 PHE 0.014 0.001 PHE B 395 TYR 0.015 0.001 TYR D 377 ARG 0.005 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 2.890 Fit side-chains REVERT: B 375 MET cc_start: 0.8567 (tpp) cc_final: 0.8090 (tmm) REVERT: D 389 MET cc_start: 0.6612 (ttt) cc_final: 0.6138 (tmm) REVERT: G 131 MET cc_start: 0.6841 (mmm) cc_final: 0.6396 (mmm) outliers start: 11 outliers final: 9 residues processed: 121 average time/residue: 0.3395 time to fit residues: 68.7993 Evaluate side-chains 116 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 191 optimal weight: 0.0370 chunk 77 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 279 optimal weight: 0.0170 chunk 96 optimal weight: 8.9990 chunk 226 optimal weight: 0.0670 overall best weight: 1.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24655 Z= 0.171 Angle : 0.494 9.665 33433 Z= 0.252 Chirality : 0.043 0.161 3852 Planarity : 0.004 0.047 4362 Dihedral : 7.691 116.578 3547 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.66 % Allowed : 8.29 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3115 helix: 1.32 (0.15), residues: 1250 sheet: 0.75 (0.23), residues: 522 loop : -0.02 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.016 0.001 PHE B 395 TYR 0.015 0.001 TYR D 377 ARG 0.010 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 2.874 Fit side-chains REVERT: B 62 MET cc_start: 0.8430 (tpp) cc_final: 0.7931 (ttt) REVERT: D 378 LYS cc_start: 0.6950 (tptt) cc_final: 0.6706 (mmtp) REVERT: D 389 MET cc_start: 0.6622 (ttt) cc_final: 0.6259 (tmm) REVERT: E 407 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8662 (tm-30) REVERT: G 67 MET cc_start: 0.7463 (mmm) cc_final: 0.7124 (mmp) REVERT: G 131 MET cc_start: 0.7049 (mmm) cc_final: 0.6655 (mmm) outliers start: 17 outliers final: 9 residues processed: 131 average time/residue: 0.3388 time to fit residues: 74.1226 Evaluate side-chains 119 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS D 375 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24655 Z= 0.341 Angle : 0.573 9.536 33433 Z= 0.294 Chirality : 0.045 0.152 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.818 124.426 3547 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.56 % Allowed : 9.81 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3115 helix: 1.09 (0.15), residues: 1239 sheet: 0.66 (0.24), residues: 505 loop : -0.16 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 470 PHE 0.017 0.002 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 3.085 Fit side-chains REVERT: A 157 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8637 (m) REVERT: D 381 GLN cc_start: 0.6089 (mm-40) cc_final: 0.5309 (tt0) REVERT: E 407 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8706 (tm-30) REVERT: G 25 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: G 131 MET cc_start: 0.7030 (mmm) cc_final: 0.6678 (mmm) outliers start: 40 outliers final: 24 residues processed: 143 average time/residue: 0.3157 time to fit residues: 76.9390 Evaluate side-chains 133 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 24655 Z= 0.503 Angle : 0.672 9.427 33433 Z= 0.347 Chirality : 0.049 0.238 3852 Planarity : 0.005 0.052 4362 Dihedral : 8.024 137.691 3547 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.02 % Allowed : 10.98 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3115 helix: 0.59 (0.14), residues: 1245 sheet: 0.37 (0.23), residues: 528 loop : -0.48 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.021 0.002 PHE B 395 TYR 0.017 0.002 TYR B 438 ARG 0.006 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 2.834 Fit side-chains revert: symmetry clash REVERT: B 236 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8882 (t80) REVERT: B 298 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8988 (mp) REVERT: C 487 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4868 (pp) REVERT: E 407 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8742 (tm-30) REVERT: G 67 MET cc_start: 0.7616 (mmm) cc_final: 0.7189 (mmp) outliers start: 52 outliers final: 35 residues processed: 149 average time/residue: 0.3159 time to fit residues: 80.4426 Evaluate side-chains 144 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 433 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24655 Z= 0.181 Angle : 0.506 9.681 33433 Z= 0.259 Chirality : 0.043 0.153 3852 Planarity : 0.004 0.050 4362 Dihedral : 7.356 133.225 3547 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.48 % Allowed : 11.99 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3115 helix: 1.13 (0.15), residues: 1237 sheet: 0.51 (0.24), residues: 515 loop : -0.21 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.016 0.001 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7734 (p0) REVERT: E 407 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8796 (tm-30) REVERT: F 64 MET cc_start: 0.9319 (mmp) cc_final: 0.8989 (mmp) REVERT: F 285 MET cc_start: 0.8815 (ttp) cc_final: 0.8538 (ttm) REVERT: G 25 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: G 67 MET cc_start: 0.7501 (mmm) cc_final: 0.7072 (mmp) REVERT: G 241 MET cc_start: 0.8341 (ptt) cc_final: 0.8066 (tmm) outliers start: 38 outliers final: 30 residues processed: 142 average time/residue: 0.3255 time to fit residues: 78.6779 Evaluate side-chains 140 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.0670 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 0.0980 chunk 169 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 overall best weight: 3.8324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 433 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24655 Z= 0.329 Angle : 0.559 9.470 33433 Z= 0.287 Chirality : 0.045 0.154 3852 Planarity : 0.004 0.050 4362 Dihedral : 7.384 133.895 3547 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.41 % Allowed : 12.19 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3115 helix: 1.04 (0.15), residues: 1239 sheet: 0.50 (0.24), residues: 508 loop : -0.32 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS G 107 PHE 0.028 0.001 PHE G 165 TYR 0.014 0.001 TYR B 248 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 109 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7809 (p0) REVERT: B 236 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8620 (t80) REVERT: B 407 GLN cc_start: 0.8111 (mt0) cc_final: 0.7910 (mp10) REVERT: C 487 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4737 (pp) REVERT: E 407 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8776 (tm-30) REVERT: F 64 MET cc_start: 0.9351 (mmp) cc_final: 0.9049 (mmt) REVERT: F 136 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8082 (pt0) outliers start: 62 outliers final: 45 residues processed: 161 average time/residue: 0.3294 time to fit residues: 91.2610 Evaluate side-chains 157 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24655 Z= 0.221 Angle : 0.516 9.567 33433 Z= 0.263 Chirality : 0.043 0.152 3852 Planarity : 0.004 0.053 4362 Dihedral : 7.157 132.634 3547 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.26 % Allowed : 12.19 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3115 helix: 1.16 (0.15), residues: 1237 sheet: 0.51 (0.24), residues: 515 loop : -0.26 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.014 0.001 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 112 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 236 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8654 (t80) REVERT: B 407 GLN cc_start: 0.8099 (mt0) cc_final: 0.7899 (mp10) REVERT: C 487 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4645 (pp) REVERT: E 407 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8787 (tm-30) REVERT: F 64 MET cc_start: 0.9321 (mmp) cc_final: 0.8946 (mmp) REVERT: F 136 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: G 67 MET cc_start: 0.7482 (mmm) cc_final: 0.7059 (mmp) outliers start: 58 outliers final: 43 residues processed: 162 average time/residue: 0.3205 time to fit residues: 88.7209 Evaluate side-chains 155 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 108 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24655 Z= 0.399 Angle : 0.601 9.361 33433 Z= 0.309 Chirality : 0.046 0.154 3852 Planarity : 0.004 0.051 4362 Dihedral : 7.308 137.016 3547 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.26 % Allowed : 11.99 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3115 helix: 0.85 (0.15), residues: 1243 sheet: 0.44 (0.24), residues: 518 loop : -0.43 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.017 0.002 PHE B 395 TYR 0.022 0.002 TYR G 171 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 110 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7848 (p0) REVERT: B 236 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8841 (t80) REVERT: C 487 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4750 (pp) REVERT: E 407 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8763 (tm-30) REVERT: F 136 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: G 67 MET cc_start: 0.7613 (mmm) cc_final: 0.7127 (mmp) outliers start: 58 outliers final: 50 residues processed: 160 average time/residue: 0.3151 time to fit residues: 86.6723 Evaluate side-chains 163 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 109 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 8.9990 chunk 294 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 433 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24655 Z= 0.238 Angle : 0.526 9.532 33433 Z= 0.268 Chirality : 0.043 0.152 3852 Planarity : 0.004 0.055 4362 Dihedral : 6.942 135.818 3547 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 12.38 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3115 helix: 1.08 (0.15), residues: 1237 sheet: 0.49 (0.24), residues: 515 loop : -0.35 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.014 0.001 PHE B 395 TYR 0.018 0.001 TYR G 171 ARG 0.004 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 109 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7761 (p0) REVERT: B 236 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8709 (t80) REVERT: C 487 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4690 (pp) REVERT: E 407 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8771 (tm-30) REVERT: F 64 MET cc_start: 0.9325 (mmp) cc_final: 0.9051 (mmt) REVERT: F 136 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: G 67 MET cc_start: 0.7512 (mmm) cc_final: 0.7037 (mmp) outliers start: 54 outliers final: 46 residues processed: 156 average time/residue: 0.3147 time to fit residues: 83.4084 Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 108 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 433 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057207 restraints weight = 72980.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059184 restraints weight = 35796.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.060452 restraints weight = 22338.992| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24655 Z= 0.299 Angle : 0.550 9.453 33433 Z= 0.281 Chirality : 0.044 0.152 3852 Planarity : 0.004 0.054 4362 Dihedral : 6.892 135.702 3547 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.30 % Allowed : 12.31 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3115 helix: 1.03 (0.15), residues: 1236 sheet: 0.46 (0.24), residues: 515 loop : -0.41 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.015 0.001 PHE B 395 TYR 0.016 0.001 TYR G 171 ARG 0.004 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.75 seconds wall clock time: 66 minutes 29.40 seconds (3989.40 seconds total)