Starting phenix.real_space_refine on Fri Aug 7 18:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev8_19994/08_2026/9ev8_19994.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev8_19994/08_2026/9ev8_19994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ev8_19994/08_2026/9ev8_19994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev8_19994/08_2026/9ev8_19994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ev8_19994/08_2026/9ev8_19994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev8_19994/08_2026/9ev8_19994.map" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.098 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 Ca 10 9.91 5 P 5 5.49 5 S 55 5.16 5 C 15111 2.51 5 N 3679 2.21 5 O 4530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23390 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4534 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 549} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4524 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 549} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4524 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 549} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4524 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 549} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4524 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 549} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 109 Unusual residues: {' CA': 2, 'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {' CA': 2, 'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 109 Unusual residues: {' CA': 2, 'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 109 Unusual residues: {' CA': 2, 'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {' CA': 2, 'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 5.64, per 1000 atoms: 0.24 Number of scatterers: 23390 At special positions: 0 Unit cell: (137.117, 139.656, 154.045, 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) Ca 10 19.99 S 55 16.00 P 5 15.00 O 4530 8.00 N 3679 7.00 C 15111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 973.1 milliseconds 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5320 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 30 sheets defined 30.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.505A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 310 through 314 removed outlier: 4.113A pdb=" N SER A 314 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.960A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.682A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 removed outlier: 3.501A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.522A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 98 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.505A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 310 through 314 removed outlier: 4.113A pdb=" N SER B 314 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.960A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.683A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.502A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.521A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 636 Proline residue: B 621 - end of helix Processing helix chain 'C' and resid 88 through 98 removed outlier: 3.815A pdb=" N GLN C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.505A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.113A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.960A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.682A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 564 removed outlier: 3.502A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.522A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 636 Proline residue: C 621 - end of helix Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.817A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.505A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.112A pdb=" N SER D 314 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.960A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.683A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 564 removed outlier: 3.501A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.521A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 98 removed outlier: 3.815A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 118 removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.113A pdb=" N SER E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.960A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.682A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 564 removed outlier: 3.502A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.522A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 Proline residue: E 621 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.687A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.504A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.353A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.065A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.687A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 211 Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.503A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.353A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.064A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.687A pdb=" N GLY C 120 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 79 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY C 141 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 57 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 204 through 211 Processing sheet with id=AB7, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.504A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.354A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.065A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.687A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 204 through 211 Processing sheet with id=AC4, first strand: chain 'D' and resid 218 through 222 removed outlier: 7.504A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.353A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.066A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 204 through 211 Processing sheet with id=AD1, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.504A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.354A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.065A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 2940 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: 5.11 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3815 1.32 - 1.44: 6294 1.44 - 1.56: 13441 1.56 - 1.69: 10 1.69 - 1.81: 80 Bond restraints: 23640 Sorted by residual: bond pdb=" C20 PX6 C 707 " pdb=" O7 PX6 C 707 " ideal model delta sigma weight residual 1.329 1.459 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C20 PX6 D 707 " pdb=" O7 PX6 D 707 " ideal model delta sigma weight residual 1.329 1.458 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C20 PX6 E 710 " pdb=" O7 PX6 E 710 " ideal model delta sigma weight residual 1.329 1.458 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C20 PX6 E 703 " pdb=" O7 PX6 E 703 " ideal model delta sigma weight residual 1.329 1.458 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C20 PX6 A 709 " pdb=" O7 PX6 A 709 " ideal model delta sigma weight residual 1.329 1.458 -0.129 2.00e-02 2.50e+03 4.17e+01 ... (remaining 23635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 31599 2.38 - 4.76: 326 4.76 - 7.15: 42 7.15 - 9.53: 11 9.53 - 11.91: 13 Bond angle restraints: 31991 Sorted by residual: angle pdb=" N GLY C 253 " pdb=" CA GLY C 253 " pdb=" C GLY C 253 " ideal model delta sigma weight residual 113.18 101.27 11.91 2.37e+00 1.78e-01 2.53e+01 angle pdb=" N GLY B 253 " pdb=" CA GLY B 253 " pdb=" C GLY B 253 " ideal model delta sigma weight residual 113.18 101.51 11.67 2.37e+00 1.78e-01 2.43e+01 angle pdb=" N GLY D 253 " pdb=" CA GLY D 253 " pdb=" C GLY D 253 " ideal model delta sigma weight residual 113.18 101.92 11.26 2.37e+00 1.78e-01 2.26e+01 angle pdb=" N TYR E 620 " pdb=" CA TYR E 620 " pdb=" C TYR E 620 " ideal model delta sigma weight residual 113.25 118.98 -5.73 1.30e+00 5.92e-01 1.94e+01 angle pdb=" N TYR D 620 " pdb=" CA TYR D 620 " pdb=" C TYR D 620 " ideal model delta sigma weight residual 113.25 118.96 -5.71 1.30e+00 5.92e-01 1.93e+01 ... (remaining 31986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 13142 14.66 - 29.32: 520 29.32 - 43.97: 191 43.97 - 58.63: 62 58.63 - 73.29: 14 Dihedral angle restraints: 13929 sinusoidal: 5649 harmonic: 8280 Sorted by residual: dihedral pdb=" CA ILE E 522 " pdb=" C ILE E 522 " pdb=" N PHE E 523 " pdb=" CA PHE E 523 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE A 522 " pdb=" C ILE A 522 " pdb=" N PHE A 523 " pdb=" CA PHE A 523 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE C 522 " pdb=" C ILE C 522 " pdb=" N PHE C 523 " pdb=" CA PHE C 523 " ideal model delta harmonic sigma weight residual 180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 13926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2978 0.053 - 0.106: 504 0.106 - 0.159: 123 0.159 - 0.211: 0 0.211 - 0.264: 5 Chirality restraints: 3610 Sorted by residual: chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR B 620 " pdb=" N TYR B 620 " pdb=" C TYR B 620 " pdb=" CB TYR B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR D 620 " pdb=" N TYR D 620 " pdb=" C TYR D 620 " pdb=" CB TYR D 620 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3607 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 619 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ILE D 619 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE D 619 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR D 620 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 619 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C ILE E 619 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE E 619 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR E 620 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 619 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C ILE A 619 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 619 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 620 " -0.012 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 115 2.55 - 3.14: 17038 3.14 - 3.72: 33510 3.72 - 4.31: 48310 4.31 - 4.90: 82222 Nonbonded interactions: 181195 Sorted by model distance: nonbonded pdb=" OD1 ASP A 123 " pdb="CA CA A 701 " model vdw 1.963 2.510 nonbonded pdb=" OD1 ASP D 123 " pdb="CA CA D 701 " model vdw 1.963 2.510 nonbonded pdb=" OD1 ASP B 123 " pdb="CA CA B 701 " model vdw 1.963 2.510 nonbonded pdb=" OD1 ASP C 123 " pdb="CA CA C 701 " model vdw 1.963 2.510 nonbonded pdb=" OD1 ASP E 123 " pdb="CA CA E 704 " model vdw 1.963 2.510 ... (remaining 181190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 254 or (resid 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 through 425 or (resid 426 and (name N o \ r name CA or name C or name O or name CB )) or resid 427 through 702)) selection = (chain 'B' and resid 37 through 702) selection = (chain 'C' and resid 37 through 702) selection = (chain 'D' and resid 37 through 702) selection = (chain 'E' and resid 37 through 702) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.670 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 23640 Z= 0.269 Angle : 0.662 11.912 31991 Z= 0.339 Chirality : 0.043 0.264 3610 Planarity : 0.004 0.032 4076 Dihedral : 10.198 73.289 8609 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.28 % Allowed : 2.31 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 2830 helix: 2.10 (0.21), residues: 690 sheet: 1.11 (0.16), residues: 920 loop : -0.54 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 406 TYR 0.011 0.001 TYR E 517 PHE 0.010 0.001 PHE B 414 TRP 0.004 0.001 TRP C 359 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.27 (23640) covalent geometry : angle 0.66189 / 0.34 (31991) hydrogen bonds : bond 0.18143 / 12.09 ( 1060) hydrogen bonds : angle 6.24038 / 4.35 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 314 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.7176 (tttt) cc_final: 0.6965 (ttmp) REVERT: A 439 LEU cc_start: 0.6779 (tp) cc_final: 0.6503 (tp) REVERT: A 514 ASN cc_start: 0.7192 (t0) cc_final: 0.6670 (m110) REVERT: A 626 LEU cc_start: 0.7701 (mt) cc_final: 0.7422 (mp) REVERT: B 439 LEU cc_start: 0.6788 (tp) cc_final: 0.6583 (mt) REVERT: C 439 LEU cc_start: 0.6799 (tp) cc_final: 0.6592 (mt) REVERT: D 338 GLN cc_start: 0.4823 (tt0) cc_final: 0.4514 (pt0) outliers start: 7 outliers final: 0 residues processed: 320 average time/residue: 0.5924 time to fit residues: 215.8834 Evaluate side-chains 150 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN B 360 HIS C 338 GLN C 360 HIS D 360 HIS E 360 HIS E 403 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.261181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.239518 restraints weight = 14447.578| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 0.45 r_work: 0.4396 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.4344 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23640 Z= 0.305 Angle : 0.792 9.676 31991 Z= 0.437 Chirality : 0.051 0.251 3610 Planarity : 0.006 0.075 4076 Dihedral : 9.337 59.887 3466 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.18 % Allowed : 6.11 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 2830 helix: 1.51 (0.19), residues: 725 sheet: 0.97 (0.16), residues: 880 loop : -0.57 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 513 TYR 0.034 0.003 TYR C 143 PHE 0.022 0.003 PHE D 399 TRP 0.010 0.002 TRP C 359 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.31 (23640) covalent geometry : angle 0.79207 / 0.44 (31991) hydrogen bonds : bond 0.08890 / 6.08 ( 1060) hydrogen bonds : angle 5.38417 / 3.72 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: B 515 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8284 (mm) REVERT: C 460 MET cc_start: 0.7975 (mtp) cc_final: 0.7731 (ttm) REVERT: C 515 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8392 (mm) REVERT: D 460 MET cc_start: 0.7876 (mtp) cc_final: 0.7640 (ttm) REVERT: D 515 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8398 (mm) REVERT: E 515 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 54 outliers final: 7 residues processed: 243 average time/residue: 0.5819 time to fit residues: 161.1239 Evaluate side-chains 179 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 239 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 220 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 262 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS C 360 HIS D 360 HIS E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.263481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.242455 restraints weight = 14763.062| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 0.45 r_work: 0.4429 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.4377 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23640 Z= 0.150 Angle : 0.539 9.836 31991 Z= 0.294 Chirality : 0.044 0.168 3610 Planarity : 0.004 0.048 4076 Dihedral : 8.220 59.599 3466 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.89 % Allowed : 8.50 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 2830 helix: 1.93 (0.20), residues: 725 sheet: 1.28 (0.16), residues: 865 loop : -0.40 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 498 TYR 0.015 0.001 TYR C 518 PHE 0.049 0.002 PHE B 561 TRP 0.007 0.001 TRP B 615 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (23640) covalent geometry : angle 0.53911 / 0.29 (31991) hydrogen bonds : bond 0.05922 / 4.05 ( 1060) hydrogen bonds : angle 4.65321 / 3.21 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.2495 (mmm) cc_final: 0.2279 (mtt) REVERT: A 460 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: B 515 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8254 (mm) REVERT: C 416 THR cc_start: 0.7991 (m) cc_final: 0.7750 (p) REVERT: C 460 MET cc_start: 0.7930 (mtp) cc_final: 0.7673 (ttm) REVERT: C 515 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8372 (mm) REVERT: D 460 MET cc_start: 0.7822 (mtp) cc_final: 0.7583 (ttm) REVERT: D 515 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8365 (mm) REVERT: E 515 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8342 (mm) outliers start: 22 outliers final: 1 residues processed: 192 average time/residue: 0.6162 time to fit residues: 134.8102 Evaluate side-chains 168 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 21 optimal weight: 0.0040 chunk 280 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS D 360 HIS D 611 GLN E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.260509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.239081 restraints weight = 14426.556| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 0.44 r_work: 0.4402 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.4351 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23640 Z= 0.211 Angle : 0.632 12.291 31991 Z= 0.347 Chirality : 0.047 0.237 3610 Planarity : 0.005 0.048 4076 Dihedral : 8.548 59.920 3466 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.38 % Allowed : 9.02 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 2830 helix: 2.16 (0.20), residues: 695 sheet: 0.99 (0.16), residues: 890 loop : -0.27 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 521 TYR 0.023 0.002 TYR E 518 PHE 0.045 0.002 PHE B 561 TRP 0.011 0.002 TRP D 534 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.21 (23640) covalent geometry : angle 0.63202 / 0.35 (31991) hydrogen bonds : bond 0.07835 / 5.37 ( 1060) hydrogen bonds : angle 4.79551 / 3.31 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 460 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: B 515 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8284 (mm) REVERT: C 460 MET cc_start: 0.8023 (mtp) cc_final: 0.7769 (ttm) REVERT: C 515 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8341 (mm) REVERT: D 58 MET cc_start: 0.2766 (ptt) cc_final: 0.2153 (mmp) REVERT: D 460 MET cc_start: 0.7888 (mtp) cc_final: 0.7654 (ttm) REVERT: D 515 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8325 (mm) REVERT: D 569 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6492 (mpp-170) REVERT: E 515 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8392 (mm) outliers start: 34 outliers final: 5 residues processed: 190 average time/residue: 0.6120 time to fit residues: 131.7557 Evaluate side-chains 166 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 20 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 121 optimal weight: 0.0970 chunk 227 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS B 560 ASN D 611 GLN E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.248535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.217436 restraints weight = 14195.137| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 0.58 r_work: 0.4044 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3771 rms_B_bonded: 3.93 restraints_weight: 0.1250 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23640 Z= 0.168 Angle : 0.564 10.614 31991 Z= 0.308 Chirality : 0.045 0.173 3610 Planarity : 0.004 0.046 4076 Dihedral : 8.059 59.829 3466 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.13 % Allowed : 9.51 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 2830 helix: 2.33 (0.20), residues: 695 sheet: 1.09 (0.17), residues: 880 loop : -0.24 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 521 TYR 0.020 0.002 TYR C 518 PHE 0.032 0.002 PHE B 561 TRP 0.007 0.001 TRP C 359 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (23640) covalent geometry : angle 0.56377 / 0.31 (31991) hydrogen bonds : bond 0.06482 / 4.45 ( 1060) hydrogen bonds : angle 4.53519 / 3.14 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: A 460 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: A 605 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6522 (mttt) REVERT: B 515 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8508 (mm) REVERT: C 460 MET cc_start: 0.8448 (mtp) cc_final: 0.8116 (ttm) REVERT: C 515 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8571 (mm) REVERT: D 58 MET cc_start: 0.2999 (ptt) cc_final: 0.1757 (mmp) REVERT: D 460 MET cc_start: 0.8400 (mtp) cc_final: 0.8079 (ttm) REVERT: D 515 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8583 (mm) REVERT: E 58 MET cc_start: 0.2591 (ptt) cc_final: 0.2335 (mpp) REVERT: E 515 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8555 (mm) outliers start: 28 outliers final: 5 residues processed: 180 average time/residue: 0.5999 time to fit residues: 122.4557 Evaluate side-chains 165 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 98 optimal weight: 0.8980 chunk 280 optimal weight: 0.9990 chunk 269 optimal weight: 0.4980 chunk 90 optimal weight: 0.0010 chunk 28 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS D 360 HIS D 611 GLN E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.250704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.219659 restraints weight = 14576.844| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 0.59 r_work: 0.4078 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 1.51 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23640 Z= 0.129 Angle : 0.502 9.313 31991 Z= 0.272 Chirality : 0.043 0.173 3610 Planarity : 0.004 0.042 4076 Dihedral : 7.543 59.496 3466 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.73 % Allowed : 9.99 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.15), residues: 2830 helix: 2.54 (0.20), residues: 695 sheet: 1.22 (0.17), residues: 880 loop : -0.09 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 521 TYR 0.015 0.001 TYR B 487 PHE 0.051 0.002 PHE C 561 TRP 0.006 0.001 TRP C 359 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (23640) covalent geometry : angle 0.50156 / 0.27 (31991) hydrogen bonds : bond 0.05329 / 3.64 ( 1060) hydrogen bonds : angle 4.27310 / 2.95 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7843 (ttm) REVERT: B 515 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8252 (mm) REVERT: C 460 MET cc_start: 0.8105 (mtp) cc_final: 0.7789 (ttm) REVERT: D 58 MET cc_start: 0.2985 (ptt) cc_final: 0.1997 (mmp) REVERT: D 460 MET cc_start: 0.8021 (mtp) cc_final: 0.7740 (ttm) REVERT: D 515 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8358 (mm) REVERT: E 515 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8345 (mm) outliers start: 18 outliers final: 5 residues processed: 167 average time/residue: 0.6113 time to fit residues: 115.8718 Evaluate side-chains 164 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 274 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS B 360 HIS D 360 HIS D 611 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.246164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.214485 restraints weight = 14168.027| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 0.58 r_work: 0.4017 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23640 Z= 0.226 Angle : 0.642 9.374 31991 Z= 0.354 Chirality : 0.048 0.193 3610 Planarity : 0.005 0.051 4076 Dihedral : 8.335 58.894 3466 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.81 % Allowed : 10.07 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 2830 helix: 2.20 (0.20), residues: 695 sheet: 1.04 (0.17), residues: 890 loop : -0.16 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 521 TYR 0.025 0.002 TYR D 518 PHE 0.034 0.003 PHE A 561 TRP 0.010 0.002 TRP D 534 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.23 (23640) covalent geometry : angle 0.64156 / 0.35 (31991) hydrogen bonds : bond 0.07986 / 5.49 ( 1060) hydrogen bonds : angle 4.70582 / 3.25 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2471 (mmm) REVERT: A 379 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 460 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7877 (ttm) REVERT: B 515 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8290 (mm) REVERT: C 460 MET cc_start: 0.8206 (mtp) cc_final: 0.7915 (ttm) REVERT: C 515 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8585 (tt) REVERT: D 58 MET cc_start: 0.3209 (ptt) cc_final: 0.2035 (mmp) REVERT: D 460 MET cc_start: 0.8037 (mtp) cc_final: 0.7768 (ttm) REVERT: D 515 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8383 (mm) REVERT: D 569 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6642 (mpp-170) REVERT: E 515 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8411 (mm) outliers start: 20 outliers final: 2 residues processed: 169 average time/residue: 0.6411 time to fit residues: 123.2133 Evaluate side-chains 160 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 4.9990 chunk 187 optimal weight: 0.0040 chunk 1 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 235 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS D 360 HIS D 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.248482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.217110 restraints weight = 14270.749| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 0.56 r_work: 0.4059 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.4017 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3802 rms_B_bonded: 3.77 restraints_weight: 0.1250 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23640 Z= 0.154 Angle : 0.539 9.032 31991 Z= 0.294 Chirality : 0.044 0.174 3610 Planarity : 0.004 0.045 4076 Dihedral : 7.787 58.829 3466 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.53 % Allowed : 10.32 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 2830 helix: 2.42 (0.20), residues: 695 sheet: 1.12 (0.17), residues: 890 loop : -0.13 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 521 TYR 0.017 0.001 TYR C 518 PHE 0.058 0.002 PHE C 561 TRP 0.007 0.001 TRP C 359 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (23640) covalent geometry : angle 0.53943 / 0.29 (31991) hydrogen bonds : bond 0.06141 / 4.20 ( 1060) hydrogen bonds : angle 4.41540 / 3.06 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.3230 (mpp) cc_final: 0.2412 (mmm) REVERT: A 460 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: B 515 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8456 (mm) REVERT: C 460 MET cc_start: 0.8449 (mtp) cc_final: 0.8119 (ttm) REVERT: C 515 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8757 (tt) REVERT: D 58 MET cc_start: 0.3104 (ptt) cc_final: 0.1764 (mmp) REVERT: D 460 MET cc_start: 0.8340 (mtp) cc_final: 0.8054 (ttm) REVERT: D 515 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8566 (mm) REVERT: D 569 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6713 (mpp-170) REVERT: E 515 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8526 (mm) outliers start: 13 outliers final: 2 residues processed: 164 average time/residue: 0.6514 time to fit residues: 121.1317 Evaluate side-chains 163 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 241 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS D 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.246649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.214010 restraints weight = 14064.663| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 0.59 r_work: 0.4006 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23640 Z= 0.249 Angle : 0.679 9.308 31991 Z= 0.375 Chirality : 0.049 0.205 3610 Planarity : 0.005 0.057 4076 Dihedral : 8.622 59.812 3466 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.69 % Allowed : 10.40 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 2830 helix: 2.08 (0.19), residues: 695 sheet: 0.97 (0.17), residues: 890 loop : -0.21 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 521 TYR 0.027 0.002 TYR E 518 PHE 0.029 0.003 PHE C 561 TRP 0.012 0.002 TRP C 407 HIS 0.007 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.25 (23640) covalent geometry : angle 0.67931 / 0.38 (31991) hydrogen bonds : bond 0.08424 / 5.79 ( 1060) hydrogen bonds : angle 4.81074 / 3.33 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.3195 (OUTLIER) cc_final: 0.2519 (mmm) REVERT: A 379 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 460 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7888 (ttm) REVERT: B 515 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8312 (mm) REVERT: C 58 MET cc_start: 0.3086 (ptt) cc_final: 0.2513 (mtm) REVERT: C 460 MET cc_start: 0.8226 (mtp) cc_final: 0.7944 (ttm) REVERT: C 515 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8618 (tt) REVERT: D 460 MET cc_start: 0.8069 (mtp) cc_final: 0.7810 (ttm) REVERT: D 515 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8405 (mm) REVERT: D 569 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6657 (mpp-170) REVERT: E 515 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8447 (mm) outliers start: 17 outliers final: 5 residues processed: 162 average time/residue: 0.6806 time to fit residues: 123.7922 Evaluate side-chains 162 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 250 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS C 360 HIS D 611 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.247069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.215962 restraints weight = 14177.642| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 0.56 r_work: 0.4037 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work: 0.3738 rms_B_bonded: 3.99 restraints_weight: 0.1250 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23640 Z= 0.199 Angle : 0.609 9.229 31991 Z= 0.335 Chirality : 0.047 0.202 3610 Planarity : 0.005 0.050 4076 Dihedral : 8.289 58.930 3466 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.53 % Allowed : 10.64 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 2830 helix: 2.22 (0.20), residues: 695 sheet: 0.98 (0.17), residues: 890 loop : -0.18 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 521 TYR 0.022 0.002 TYR C 518 PHE 0.055 0.002 PHE D 561 TRP 0.010 0.002 TRP C 407 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.20 (23640) covalent geometry : angle 0.60936 / 0.34 (31991) hydrogen bonds : bond 0.07230 / 4.97 ( 1060) hydrogen bonds : angle 4.65915 / 3.22 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.3158 (OUTLIER) cc_final: 0.2472 (mmm) REVERT: A 379 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 460 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8118 (ttm) REVERT: B 515 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8501 (mm) REVERT: C 58 MET cc_start: 0.3158 (ptt) cc_final: 0.1819 (mmp) REVERT: C 460 MET cc_start: 0.8516 (mtp) cc_final: 0.8199 (ttm) REVERT: C 515 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8783 (tt) REVERT: D 58 MET cc_start: 0.3085 (ptt) cc_final: 0.1581 (mmp) REVERT: D 460 MET cc_start: 0.8398 (mtp) cc_final: 0.8132 (ttm) REVERT: D 515 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8616 (mm) REVERT: D 569 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6803 (mpp-170) REVERT: E 515 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8565 (mm) outliers start: 13 outliers final: 4 residues processed: 158 average time/residue: 0.6685 time to fit residues: 119.7601 Evaluate side-chains 161 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 259 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.0040 chunk 98 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS C 360 HIS D 611 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.246964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.216308 restraints weight = 14160.840| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 0.58 r_work: 0.4040 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23640 Z= 0.197 Angle : 0.605 9.157 31991 Z= 0.333 Chirality : 0.046 0.211 3610 Planarity : 0.005 0.046 4076 Dihedral : 8.220 59.489 3466 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.53 % Allowed : 10.72 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 2830 helix: 2.24 (0.20), residues: 695 sheet: 1.01 (0.17), residues: 890 loop : -0.17 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 521 TYR 0.022 0.002 TYR C 518 PHE 0.057 0.002 PHE D 561 TRP 0.014 0.002 TRP C 407 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.20 (23640) covalent geometry : angle 0.60499 / 0.33 (31991) hydrogen bonds : bond 0.07289 / 5.00 ( 1060) hydrogen bonds : angle 4.63249 / 3.20 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9254.67 seconds wall clock time: 157 minutes 22.62 seconds (9442.62 seconds total)