Starting phenix.real_space_refine on Sat Jul 4 20:22:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev8_19994/07_2026/9ev8_19994.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev8_19994/07_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_19994/07_2026/9ev8_19994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev8_19994/07_2026/9ev8_19994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ev8_19994/07_2026/9ev8_19994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev8_19994/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 107 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 1} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 2 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, 64 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 2 Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 107 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 1} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 2 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, 107 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 1} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 2 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, 150 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 2, 'PX6': 2} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 2 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: 4.38, per 1000 atoms: 0.19 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: 1.92 Conformation dependent library (CDL) restraints added in 754.5 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: 0.70 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: 3.51 Time building geometry restraints manager: 2.28 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 3.250 nonbonded pdb=" OD1 ASP D 123 " pdb="CA CA D 701 " model vdw 1.963 3.250 nonbonded pdb=" OD1 ASP B 123 " pdb="CA CA B 701 " model vdw 1.963 3.250 nonbonded pdb=" OD1 ASP C 123 " pdb="CA CA C 701 " model vdw 1.963 3.250 nonbonded pdb=" OD1 ASP E 123 " pdb="CA CA E 704 " model vdw 1.963 3.250 ... (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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.040 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- 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 : 0.864 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: 0.6995 time to fit residues: 254.2680 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 : 0.798 ------------------------------------------------------------------------------- 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: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.261271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.239359 restraints weight = 14498.078| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 0.43 r_work: 0.4400 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.4350 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23640 Z= 0.308 Angle : 0.785 9.644 31991 Z= 0.435 Chirality : 0.051 0.256 3610 Planarity : 0.006 0.077 4076 Dihedral : 9.363 59.539 3466 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.18 % Allowed : 6.23 % Favored : 91.59 % 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: 1.53 (0.19), residues: 725 sheet: 0.97 (0.16), residues: 880 loop : -0.59 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 513 TYR 0.031 0.003 TYR D 518 PHE 0.020 0.003 PHE D 399 TRP 0.011 0.002 TRP A 534 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.31 (23640) covalent geometry : angle 0.78549 / 0.43 (31991) hydrogen bonds : bond 0.08962 / 6.13 ( 1060) hydrogen bonds : angle 5.38878 / 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 263 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7707 (ttm) REVERT: B 515 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8300 (mm) REVERT: C 460 MET cc_start: 0.8001 (mtp) cc_final: 0.7748 (ttm) REVERT: C 515 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8373 (mm) REVERT: D 460 MET cc_start: 0.7872 (mtp) cc_final: 0.7637 (ttm) REVERT: D 515 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8395 (mm) REVERT: E 515 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8439 (mm) outliers start: 54 outliers final: 8 residues processed: 241 average time/residue: 0.6963 time to fit residues: 191.0700 Evaluate side-chains 178 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 SER 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 252 SER 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 515 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 239 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 272 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 262 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS C 360 HIS C 410 ASN C 611 GLN D 360 HIS E 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.264352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.243595 restraints weight = 14936.157| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 0.43 r_work: 0.4437 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.4388 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23640 Z= 0.138 Angle : 0.531 9.756 31991 Z= 0.289 Chirality : 0.043 0.168 3610 Planarity : 0.004 0.046 4076 Dihedral : 8.255 59.844 3466 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.77 % Allowed : 8.70 % Favored : 90.53 % 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: 1.97 (0.20), residues: 725 sheet: 1.43 (0.16), residues: 910 loop : -0.47 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 521 TYR 0.014 0.001 TYR E 518 PHE 0.041 0.002 PHE D 561 TRP 0.006 0.001 TRP B 615 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (23640) covalent geometry : angle 0.53081 / 0.29 (31991) hydrogen bonds : bond 0.05799 / 3.95 ( 1060) hydrogen bonds : angle 4.66191 / 3.22 ( 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 200 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.7959 (mtm) cc_final: 0.7743 (ttm) REVERT: B 515 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8244 (mm) REVERT: C 416 THR cc_start: 0.7937 (m) cc_final: 0.7701 (p) REVERT: C 460 MET cc_start: 0.7942 (mtp) cc_final: 0.7671 (ttm) REVERT: C 515 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8339 (mm) REVERT: D 460 MET cc_start: 0.7836 (mtp) cc_final: 0.7597 (ttm) REVERT: D 515 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8359 (mm) REVERT: E 416 THR cc_start: 0.7941 (m) cc_final: 0.7718 (p) REVERT: E 515 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8335 (mm) outliers start: 19 outliers final: 1 residues processed: 192 average time/residue: 0.7248 time to fit residues: 158.1293 Evaluate side-chains 167 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0000 chunk 280 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 181 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 177 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS D 360 HIS E 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.264603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.243355 restraints weight = 14999.816| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 0.44 r_work: 0.4432 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.4383 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23640 Z= 0.127 Angle : 0.497 10.254 31991 Z= 0.269 Chirality : 0.043 0.162 3610 Planarity : 0.004 0.043 4076 Dihedral : 7.603 58.726 3466 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.09 % Allowed : 9.39 % Favored : 89.52 % 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: 1.52 (0.15), residues: 2830 helix: 2.52 (0.20), residues: 695 sheet: 1.55 (0.16), residues: 910 loop : -0.31 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 521 TYR 0.012 0.001 TYR C 517 PHE 0.037 0.002 PHE E 561 TRP 0.006 0.001 TRP C 615 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (23640) covalent geometry : angle 0.49674 / 0.27 (31991) hydrogen bonds : bond 0.05257 / 3.60 ( 1060) hydrogen bonds : angle 4.34600 / 3.00 ( 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 190 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7706 (ttm) REVERT: A 515 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8525 (mm) REVERT: B 418 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6792 (p0) REVERT: B 515 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8374 (mm) REVERT: C 460 MET cc_start: 0.7904 (mtp) cc_final: 0.7632 (ttm) REVERT: D 58 MET cc_start: 0.2356 (ptt) cc_final: 0.2010 (mmp) REVERT: D 460 MET cc_start: 0.7822 (mtp) cc_final: 0.7584 (ttm) REVERT: D 515 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8325 (mm) REVERT: E 515 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8311 (mm) outliers start: 27 outliers final: 4 residues processed: 183 average time/residue: 0.7286 time to fit residues: 151.2592 Evaluate side-chains 167 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 20 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 0.0030 chunk 155 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 overall best weight: 2.7396 ------------------------------------------------------------------------------- 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 = 0.4696 r_free = 0.4696 target = 0.259071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.237115 restraints weight = 14219.050| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 0.40 r_work: 0.4387 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4338 rms_B_bonded: 1.33 restraints_weight: 0.2500 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23640 Z= 0.272 Angle : 0.715 10.947 31991 Z= 0.395 Chirality : 0.050 0.227 3610 Planarity : 0.006 0.064 4076 Dihedral : 8.828 59.675 3466 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.50 % Allowed : 9.22 % 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: 1.03 (0.15), residues: 2830 helix: 2.04 (0.19), residues: 695 sheet: 0.95 (0.16), residues: 890 loop : -0.26 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 521 TYR 0.029 0.002 TYR C 518 PHE 0.060 0.003 PHE D 561 TRP 0.012 0.003 TRP D 534 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.27 (23640) covalent geometry : angle 0.71509 / 0.40 (31991) hydrogen bonds : bond 0.08816 / 6.05 ( 1060) hydrogen bonds : angle 4.92960 / 3.41 ( 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 197 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7746 (ttm) REVERT: B 515 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8307 (mm) REVERT: C 107 ILE cc_start: 0.4488 (OUTLIER) cc_final: 0.4235 (mt) REVERT: C 460 MET cc_start: 0.8070 (mtp) cc_final: 0.7801 (ttm) REVERT: C 515 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8588 (tt) REVERT: D 58 MET cc_start: 0.3032 (ptt) cc_final: 0.2318 (mmp) REVERT: D 460 MET cc_start: 0.7905 (mtp) cc_final: 0.7664 (ttm) REVERT: D 515 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8397 (mm) REVERT: D 569 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6547 (mpp-170) REVERT: E 515 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8421 (mm) outliers start: 37 outliers final: 4 residues processed: 185 average time/residue: 0.7083 time to fit residues: 148.9241 Evaluate side-chains 161 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS 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 107 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 416 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 98 optimal weight: 0.2980 chunk 280 optimal weight: 0.7980 chunk 269 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 HIS E 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.251320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.221191 restraints weight = 14678.822| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 0.58 r_work: 0.4090 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.4043 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23640 Z= 0.127 Angle : 0.506 9.864 31991 Z= 0.274 Chirality : 0.043 0.161 3610 Planarity : 0.004 0.043 4076 Dihedral : 7.751 59.099 3466 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.57 % Allowed : 10.52 % 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: 1.47 (0.15), residues: 2830 helix: 2.51 (0.20), residues: 695 sheet: 1.41 (0.16), residues: 870 loop : -0.20 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 521 TYR 0.014 0.001 TYR B 487 PHE 0.039 0.002 PHE E 561 TRP 0.006 0.001 TRP C 359 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (23640) covalent geometry : angle 0.50598 / 0.27 (31991) hydrogen bonds : bond 0.05391 / 3.68 ( 1060) hydrogen bonds : angle 4.33941 / 3.00 ( 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 176 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.2661 (OUTLIER) cc_final: 0.2199 (mmm) REVERT: A 460 MET cc_start: 0.8134 (mtm) cc_final: 0.7876 (ttm) REVERT: B 515 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8388 (mm) REVERT: C 460 MET cc_start: 0.8101 (mtp) cc_final: 0.7811 (ttm) REVERT: D 58 MET cc_start: 0.2905 (ptt) cc_final: 0.1942 (mmp) REVERT: D 460 MET cc_start: 0.8035 (mtp) cc_final: 0.7752 (ttm) REVERT: D 515 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8364 (mm) REVERT: E 515 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8309 (mm) outliers start: 14 outliers final: 2 residues processed: 170 average time/residue: 0.6956 time to fit residues: 133.5196 Evaluate side-chains 159 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 0.0170 chunk 248 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 overall best weight: 2.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS B 360 HIS D 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.245148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.214444 restraints weight = 14105.843| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 0.56 r_work: 0.4049 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23640 Z= 0.255 Angle : 0.691 10.521 31991 Z= 0.383 Chirality : 0.049 0.205 3610 Planarity : 0.006 0.058 4076 Dihedral : 8.671 59.141 3466 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.65 % Allowed : 10.64 % Favored : 88.71 % 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: 1.04 (0.15), residues: 2830 helix: 2.04 (0.19), residues: 695 sheet: 0.95 (0.17), residues: 890 loop : -0.24 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 521 TYR 0.028 0.002 TYR E 518 PHE 0.049 0.003 PHE A 561 TRP 0.012 0.002 TRP A 407 HIS 0.005 0.001 HIS E 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.26 (23640) covalent geometry : angle 0.69112 / 0.38 (31991) hydrogen bonds : bond 0.08591 / 5.92 ( 1060) hydrogen bonds : angle 4.82409 / 3.34 ( 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 174 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.3057 (OUTLIER) cc_final: 0.2551 (mmm) REVERT: A 460 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: B 515 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8298 (mm) REVERT: C 58 MET cc_start: 0.3030 (ptt) cc_final: 0.2035 (mmp) REVERT: C 460 MET cc_start: 0.8209 (mtp) cc_final: 0.7919 (ttm) REVERT: D 58 MET cc_start: 0.3203 (ptt) cc_final: 0.2084 (mmp) REVERT: D 460 MET cc_start: 0.8055 (mtp) cc_final: 0.7778 (ttm) REVERT: D 515 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8394 (mm) REVERT: D 629 ILE cc_start: 0.8638 (mt) cc_final: 0.8421 (mm) REVERT: E 356 LYS cc_start: 0.8325 (ttmp) cc_final: 0.8089 (tmmt) REVERT: E 515 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8427 (mm) outliers start: 16 outliers final: 3 residues processed: 167 average time/residue: 0.7195 time to fit residues: 135.6180 Evaluate side-chains 157 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 515 LEU 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: 1.9990 chunk 187 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 188 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 235 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS C 360 HIS D 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.247451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.217059 restraints weight = 14193.292| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 0.59 r_work: 0.4047 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23640 Z= 0.178 Angle : 0.581 8.926 31991 Z= 0.319 Chirality : 0.045 0.177 3610 Planarity : 0.005 0.048 4076 Dihedral : 8.132 58.965 3466 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.40 % Allowed : 11.04 % Favored : 88.55 % 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: 2.28 (0.20), residues: 695 sheet: 1.01 (0.17), residues: 890 loop : -0.20 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 521 TYR 0.022 0.002 TYR C 518 PHE 0.046 0.002 PHE E 561 TRP 0.008 0.001 TRP E 534 HIS 0.004 0.001 HIS E 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.18 (23640) covalent geometry : angle 0.58057 / 0.32 (31991) hydrogen bonds : bond 0.06798 / 4.67 ( 1060) hydrogen bonds : angle 4.56731 / 3.16 ( 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 166 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.2911 (OUTLIER) cc_final: 0.2450 (mmm) REVERT: A 460 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7847 (ttm) REVERT: B 515 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8278 (mm) REVERT: C 58 MET cc_start: 0.3025 (ptt) cc_final: 0.1924 (mmp) REVERT: C 460 MET cc_start: 0.8164 (mtp) cc_final: 0.7870 (ttm) REVERT: D 58 MET cc_start: 0.3114 (ptt) cc_final: 0.1972 (mmp) REVERT: D 460 MET cc_start: 0.8036 (mtp) cc_final: 0.7759 (ttm) REVERT: D 515 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8356 (mm) REVERT: E 515 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8387 (mm) outliers start: 10 outliers final: 3 residues processed: 160 average time/residue: 0.7469 time to fit residues: 134.6544 Evaluate side-chains 162 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 515 LEU 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: 0.3980 chunk 191 optimal weight: 0.9990 chunk 149 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS C 360 HIS D 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.249969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.219474 restraints weight = 14549.911| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 0.58 r_work: 0.4073 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3708 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23640 Z= 0.132 Angle : 0.512 8.866 31991 Z= 0.277 Chirality : 0.043 0.162 3610 Planarity : 0.004 0.043 4076 Dihedral : 7.581 59.084 3466 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.32 % Allowed : 11.37 % Favored : 88.31 % 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: 1.48 (0.16), residues: 2830 helix: 2.53 (0.20), residues: 695 sheet: 1.35 (0.17), residues: 855 loop : -0.13 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 521 TYR 0.019 0.001 TYR B 487 PHE 0.029 0.002 PHE D 561 TRP 0.007 0.001 TRP C 359 HIS 0.004 0.001 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (23640) covalent geometry : angle 0.51194 / 0.28 (31991) hydrogen bonds : bond 0.05531 / 3.79 ( 1060) hydrogen bonds : angle 4.31653 / 3.00 ( 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 166 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.2944 (OUTLIER) cc_final: 0.2387 (mmm) REVERT: A 460 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8157 (ttm) REVERT: B 515 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8566 (mm) REVERT: C 58 MET cc_start: 0.2762 (ptt) cc_final: 0.1412 (mmp) REVERT: C 460 MET cc_start: 0.8528 (mtp) cc_final: 0.8168 (ttm) REVERT: D 58 MET cc_start: 0.2984 (ptt) cc_final: 0.1525 (mmp) REVERT: D 460 MET cc_start: 0.8438 (mtp) cc_final: 0.8134 (ttm) REVERT: D 515 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8681 (mm) REVERT: E 515 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8609 (mm) outliers start: 8 outliers final: 3 residues processed: 161 average time/residue: 0.7278 time to fit residues: 132.0719 Evaluate side-chains 164 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 515 LEU 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: 6.9990 chunk 160 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS B 471 GLN C 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.243916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.211611 restraints weight = 13854.823| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 0.59 r_work: 0.3973 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 23640 Z= 0.423 Angle : 0.946 9.497 31991 Z= 0.524 Chirality : 0.059 0.351 3610 Planarity : 0.008 0.098 4076 Dihedral : 10.309 59.883 3466 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.57 % Allowed : 11.37 % Favored : 88.07 % 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: 0.36 (0.15), residues: 2830 helix: 1.24 (0.19), residues: 725 sheet: 0.52 (0.17), residues: 850 loop : -0.48 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 513 TYR 0.038 0.004 TYR E 518 PHE 0.078 0.005 PHE E 561 TRP 0.022 0.004 TRP A 615 HIS 0.006 0.002 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.42 (23640) covalent geometry : angle 0.94578 / 0.52 (31991) hydrogen bonds : bond 0.10698 / 7.34 ( 1060) hydrogen bonds : angle 5.28770 / 3.65 ( 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 173 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.3402 (OUTLIER) cc_final: 0.2778 (mmm) REVERT: A 460 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7979 (ttm) REVERT: B 515 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 460 MET cc_start: 0.8266 (mtp) cc_final: 0.7961 (ttm) REVERT: D 460 MET cc_start: 0.8146 (mtp) cc_final: 0.7859 (ttm) REVERT: D 515 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8448 (mm) REVERT: E 515 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8479 (mm) outliers start: 14 outliers final: 5 residues processed: 165 average time/residue: 0.7524 time to fit residues: 139.6596 Evaluate side-chains 162 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 319 VAL 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: 2.9990 chunk 76 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 360 HIS B 471 GLN C 360 HIS E 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.248194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.216269 restraints weight = 14374.889| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 0.57 r_work: 0.4046 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23640 Z= 0.158 Angle : 0.555 9.173 31991 Z= 0.303 Chirality : 0.044 0.164 3610 Planarity : 0.004 0.045 4076 Dihedral : 8.859 59.816 3466 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.57 % Allowed : 11.08 % Favored : 88.35 % 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: 1.04 (0.15), residues: 2830 helix: 2.24 (0.20), residues: 695 sheet: 0.81 (0.17), residues: 850 loop : -0.22 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 521 TYR 0.019 0.001 TYR B 487 PHE 0.059 0.002 PHE E 561 TRP 0.008 0.001 TRP C 407 HIS 0.004 0.001 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (23640) covalent geometry : angle 0.55474 / 0.30 (31991) hydrogen bonds : bond 0.06205 / 4.25 ( 1060) hydrogen bonds : angle 4.55523 / 3.16 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9943.28 seconds wall clock time: 169 minutes 24.80 seconds (10164.80 seconds total)