Starting phenix.real_space_refine on Thu Mar 13 09:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rjj_19243/03_2025/8rjj_19243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rjj_19243/03_2025/8rjj_19243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rjj_19243/03_2025/8rjj_19243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rjj_19243/03_2025/8rjj_19243.map" model { file = "/net/cci-nas-00/data/ceres_data/8rjj_19243/03_2025/8rjj_19243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rjj_19243/03_2025/8rjj_19243.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5464 2.51 5 N 1434 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8672 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1333 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2693 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 26, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1333 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2693 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 26, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.78, per 1000 atoms: 0.78 Number of scatterers: 8672 At special positions: 0 Unit cell: (117.008, 88.168, 97.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1706 8.00 N 1434 7.00 C 5464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 229 " - pdb=" SG CYS C 304 " distance=2.04 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 281 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 504 " distance=2.03 Simple disulfide: pdb=" SG CYS D 452 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS D 459 " - pdb=" SG CYS D 487 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 565 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 553 " distance=2.03 Simple disulfide: pdb=" SG CYS D 570 " - pdb=" SG CYS D 603 " distance=2.03 Simple disulfide: pdb=" SG CYS D 587 " - pdb=" SG CYS D 591 " distance=2.03 Simple disulfide: pdb=" SG CYS D 613 " - pdb=" SG CYS D 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.04 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 452 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 650 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG F 1 " - " ASN C 305 " " NAG I 1 " - " ASN B 448 " " NAG K 1 " - " ASN A 305 " " NAG L 1 " - " ASN D 448 " " NAG N 1 " - " ASN B 423 " " NAG O 1 " - " ASN D 557 " " NAG P 1 " - " ASN D 629 " " NAG Q 1 " - " ASN D 651 " " NAG S 1 " - " ASN B 557 " " NAG T 1 " - " ASN B 629 " " NAG U 1 " - " ASN B 651 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 18 sheets defined 31.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'C' and resid 254 through 275 removed outlier: 3.966A pdb=" N ILE C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 293 Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 330 through 350 Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 367 through 383 removed outlier: 4.030A pdb=" N VAL C 371 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 372 " --> pdb=" O TRP C 368 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 432 through 442 Processing helix chain 'D' and resid 451 through 457 Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.656A pdb=" N PHE D 465 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 630 removed outlier: 4.356A pdb=" N ASN D 629 " --> pdb=" O CYS D 626 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 630 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 734 Processing helix chain 'D' and resid 735 through 749 Processing helix chain 'A' and resid 254 through 276 removed outlier: 4.012A pdb=" N ILE A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.527A pdb=" N PHE A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 330 through 350 Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.937A pdb=" N VAL A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 372 " --> pdb=" O TRP A 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.607A pdb=" N PHE B 465 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 720 through 734 Processing helix chain 'B' and resid 735 through 749 Processing sheet with id=AA1, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA2, first strand: chain 'C' and resid 212 through 215 removed outlier: 4.017A pdb=" N VAL C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 229 through 231 Processing sheet with id=AA4, first strand: chain 'D' and resid 413 through 416 Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 515 through 517 removed outlier: 4.655A pdb=" N VAL D 507 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N MET D 556 " --> pdb=" O PRO D 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 613 through 615 removed outlier: 3.654A pdb=" N THR D 631 " --> pdb=" O CYS D 650 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 664 through 665 removed outlier: 6.146A pdb=" N ASP D 664 " --> pdb=" O PHE D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 677 through 679 removed outlier: 4.600A pdb=" N HIS D 697 " --> pdb=" O TYR D 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AB2, first strand: chain 'A' and resid 212 through 215 Processing sheet with id=AB3, first strand: chain 'A' and resid 229 through 231 Processing sheet with id=AB4, first strand: chain 'B' and resid 413 through 416 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'B' and resid 515 through 517 removed outlier: 4.678A pdb=" N VAL B 507 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N MET B 556 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 613 through 615 removed outlier: 3.521A pdb=" N THR B 631 " --> pdb=" O CYS B 650 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 664 through 665 removed outlier: 6.393A pdb=" N ASP B 664 " --> pdb=" O PHE B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 677 through 679 283 hydrogen bonds defined for protein. 795 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: 2.51 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2683 1.34 - 1.46: 2080 1.46 - 1.58: 4045 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8892 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C1 BMA S 3 " pdb=" O5 BMA S 3 " ideal model delta sigma weight residual 1.410 1.450 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sigma weight residual 1.410 1.450 -0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 8887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 11839 2.43 - 4.85: 257 4.85 - 7.27: 59 7.27 - 9.70: 6 9.70 - 12.12: 1 Bond angle restraints: 12162 Sorted by residual: angle pdb=" N PRO C 326 " pdb=" CA PRO C 326 " pdb=" CB PRO C 326 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.68e+01 angle pdb=" N PRO A 326 " pdb=" CA PRO A 326 " pdb=" CB PRO A 326 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" CB MET C 280 " pdb=" CG MET C 280 " pdb=" SD MET C 280 " ideal model delta sigma weight residual 112.70 124.82 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C TYR C 361 " pdb=" N PHE C 362 " pdb=" CA PHE C 362 " ideal model delta sigma weight residual 121.66 115.22 6.44 1.76e+00 3.23e-01 1.34e+01 angle pdb=" CB LYS B 634 " pdb=" CG LYS B 634 " pdb=" CD LYS B 634 " ideal model delta sigma weight residual 111.30 119.63 -8.33 2.30e+00 1.89e-01 1.31e+01 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.80: 5261 25.80 - 51.60: 378 51.60 - 77.39: 80 77.39 - 103.19: 52 103.19 - 128.99: 33 Dihedral angle restraints: 5804 sinusoidal: 2708 harmonic: 3096 Sorted by residual: dihedral pdb=" CA PHE B 510 " pdb=" C PHE B 510 " pdb=" N THR B 511 " pdb=" CA THR B 511 " ideal model delta harmonic sigma weight residual 180.00 142.36 37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CB CYS D 452 " pdb=" SG CYS D 452 " pdb=" SG CYS D 626 " pdb=" CB CYS D 626 " ideal model delta sinusoidal sigma weight residual 93.00 153.93 -60.93 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS C 272 " pdb=" SG CYS C 272 " pdb=" SG CYS C 281 " pdb=" CB CYS C 281 " ideal model delta sinusoidal sigma weight residual 93.00 153.46 -60.46 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1432 0.105 - 0.209: 55 0.209 - 0.314: 14 0.314 - 0.419: 1 0.419 - 0.523: 1 Chirality restraints: 1503 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 305 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN D 629 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C4 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C5 NAG K 1 " pdb=" O4 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1500 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 305 " -0.024 2.00e-02 2.50e+03 2.30e-02 6.60e+00 pdb=" CG ASN C 305 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 305 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 305 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 525 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 526 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 557 " 0.019 2.00e-02 2.50e+03 1.70e-02 3.59e+00 pdb=" CG ASN B 557 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 557 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 557 " -0.017 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.019 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 283 2.65 - 3.21: 9241 3.21 - 3.77: 14473 3.77 - 4.34: 17954 4.34 - 4.90: 27475 Nonbonded interactions: 69426 Sorted by model distance: nonbonded pdb=" O GLN D 409 " pdb=" OH TYR D 443 " model vdw 2.086 3.040 nonbonded pdb=" OD1 ASP C 232 " pdb=" OG1 THR C 235 " model vdw 2.113 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" OG1 THR A 235 " model vdw 2.117 3.040 nonbonded pdb=" O GLN B 409 " pdb=" OH TYR B 443 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASN D 423 " pdb=" OG1 THR D 425 " model vdw 2.176 3.040 ... (remaining 69421 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.830 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 0.050 8892 Z= 0.329 Angle : 0.882 12.125 12162 Z= 0.429 Chirality : 0.056 0.523 1503 Planarity : 0.005 0.054 1494 Dihedral : 22.552 128.992 3740 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.24 % Allowed : 29.81 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.27), residues: 1054 helix: 0.73 (0.31), residues: 314 sheet: -1.95 (0.46), residues: 124 loop : -1.94 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 530 HIS 0.005 0.001 HIS A 222 PHE 0.022 0.002 PHE A 285 TYR 0.019 0.002 TYR B 709 ARG 0.004 0.000 ARG D 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9214 (tmm) cc_final: 0.8567 (mmt) REVERT: D 634 LYS cc_start: 0.9534 (mmtm) cc_final: 0.9071 (mmmt) outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 0.1881 time to fit residues: 22.1727 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS D 409 GLN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.064535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047514 restraints weight = 46984.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049279 restraints weight = 27164.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050455 restraints weight = 19359.117| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8892 Z= 0.272 Angle : 0.802 9.125 12162 Z= 0.382 Chirality : 0.050 0.340 1503 Planarity : 0.005 0.052 1494 Dihedral : 17.493 114.521 2100 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 5.05 % Allowed : 22.24 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.27), residues: 1054 helix: 0.82 (0.30), residues: 322 sheet: -1.43 (0.51), residues: 98 loop : -2.04 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 530 HIS 0.004 0.001 HIS B 595 PHE 0.021 0.002 PHE D 510 TYR 0.019 0.002 TYR D 709 ARG 0.004 0.001 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9671 (tp) cc_final: 0.9458 (pp) REVERT: C 280 MET cc_start: 0.9349 (tmm) cc_final: 0.8655 (mmt) REVERT: D 634 LYS cc_start: 0.9590 (mmtm) cc_final: 0.9135 (mmmt) REVERT: B 447 PHE cc_start: 0.8231 (t80) cc_final: 0.8017 (t80) REVERT: B 530 TRP cc_start: 0.8144 (m100) cc_final: 0.7846 (m100) REVERT: B 634 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9095 (mmmm) outliers start: 42 outliers final: 19 residues processed: 112 average time/residue: 0.1504 time to fit residues: 25.7123 Evaluate side-chains 91 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN C 222 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.064910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048190 restraints weight = 47261.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049891 restraints weight = 26900.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051012 restraints weight = 18959.611| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8892 Z= 0.249 Angle : 0.781 10.595 12162 Z= 0.374 Chirality : 0.049 0.288 1503 Planarity : 0.005 0.050 1494 Dihedral : 14.318 114.759 2100 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.69 % Allowed : 23.20 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 1054 helix: 1.16 (0.31), residues: 310 sheet: -1.43 (0.50), residues: 104 loop : -2.04 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 530 HIS 0.004 0.001 HIS C 222 PHE 0.013 0.001 PHE D 510 TYR 0.020 0.002 TYR D 709 ARG 0.002 0.000 ARG D 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9653 (tp) cc_final: 0.9418 (pp) REVERT: C 280 MET cc_start: 0.9357 (tmm) cc_final: 0.9133 (tmm) REVERT: D 634 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9147 (mmmt) REVERT: B 447 PHE cc_start: 0.8163 (t80) cc_final: 0.7914 (t80) REVERT: B 528 TYR cc_start: 0.8792 (m-10) cc_final: 0.8459 (m-10) REVERT: B 634 LYS cc_start: 0.9601 (mmtm) cc_final: 0.9117 (mmmm) REVERT: B 688 MET cc_start: 0.8461 (mtp) cc_final: 0.8217 (mtp) outliers start: 39 outliers final: 22 residues processed: 113 average time/residue: 0.1660 time to fit residues: 28.5776 Evaluate side-chains 94 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 GLN A 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.065322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048595 restraints weight = 45982.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050302 restraints weight = 26233.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051443 restraints weight = 18525.644| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8892 Z= 0.214 Angle : 0.763 10.487 12162 Z= 0.366 Chirality : 0.048 0.338 1503 Planarity : 0.005 0.051 1494 Dihedral : 12.694 112.624 2100 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.21 % Allowed : 25.24 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 1054 helix: 1.26 (0.31), residues: 310 sheet: -1.55 (0.47), residues: 124 loop : -1.96 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 530 HIS 0.003 0.001 HIS B 595 PHE 0.022 0.001 PHE A 285 TYR 0.020 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9364 (tmm) cc_final: 0.9119 (tmm) REVERT: D 634 LYS cc_start: 0.9592 (mmtm) cc_final: 0.9145 (mmmt) REVERT: B 528 TYR cc_start: 0.8753 (m-10) cc_final: 0.8356 (m-10) REVERT: B 634 LYS cc_start: 0.9591 (mmtm) cc_final: 0.9095 (mmmm) REVERT: B 688 MET cc_start: 0.8437 (mtp) cc_final: 0.8184 (ttm) outliers start: 35 outliers final: 23 residues processed: 103 average time/residue: 0.2310 time to fit residues: 35.3868 Evaluate side-chains 94 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 103 optimal weight: 0.0050 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048882 restraints weight = 46083.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050618 restraints weight = 26368.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051743 restraints weight = 18578.160| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8892 Z= 0.205 Angle : 0.741 9.913 12162 Z= 0.359 Chirality : 0.048 0.295 1503 Planarity : 0.005 0.053 1494 Dihedral : 11.666 110.718 2100 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 4.93 % Allowed : 24.76 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 1054 helix: 1.27 (0.31), residues: 310 sheet: -1.72 (0.44), residues: 146 loop : -1.92 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 530 HIS 0.003 0.001 HIS B 595 PHE 0.014 0.001 PHE A 362 TYR 0.020 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 528 TYR cc_start: 0.8528 (m-10) cc_final: 0.8204 (m-10) REVERT: D 634 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9109 (mmmm) REVERT: A 280 MET cc_start: 0.9357 (tmm) cc_final: 0.8464 (mmt) REVERT: B 528 TYR cc_start: 0.8749 (m-10) cc_final: 0.8501 (m-10) REVERT: B 634 LYS cc_start: 0.9604 (mmtm) cc_final: 0.9094 (mmmm) REVERT: B 688 MET cc_start: 0.8439 (mtp) cc_final: 0.8213 (mtp) outliers start: 41 outliers final: 25 residues processed: 109 average time/residue: 0.2233 time to fit residues: 37.6429 Evaluate side-chains 101 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048502 restraints weight = 45061.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050220 restraints weight = 25934.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051376 restraints weight = 18303.826| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8892 Z= 0.218 Angle : 0.745 9.076 12162 Z= 0.360 Chirality : 0.047 0.289 1503 Planarity : 0.005 0.054 1494 Dihedral : 11.100 108.154 2100 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 4.33 % Allowed : 25.96 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.27), residues: 1054 helix: 1.25 (0.31), residues: 310 sheet: -1.36 (0.51), residues: 110 loop : -1.86 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 622 HIS 0.003 0.001 HIS B 595 PHE 0.020 0.001 PHE C 362 TYR 0.020 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 528 TYR cc_start: 0.8509 (m-10) cc_final: 0.8158 (m-10) REVERT: D 634 LYS cc_start: 0.9588 (mmtm) cc_final: 0.9111 (mmmm) REVERT: A 280 MET cc_start: 0.9370 (tmm) cc_final: 0.8452 (mmt) REVERT: B 528 TYR cc_start: 0.8694 (m-10) cc_final: 0.8429 (m-10) REVERT: B 634 LYS cc_start: 0.9599 (mmtm) cc_final: 0.9094 (mmmm) REVERT: B 688 MET cc_start: 0.8445 (mtp) cc_final: 0.8234 (mtp) outliers start: 36 outliers final: 28 residues processed: 106 average time/residue: 0.1696 time to fit residues: 26.7924 Evaluate side-chains 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 chunk 64 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047242 restraints weight = 46502.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048900 restraints weight = 26786.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050039 restraints weight = 19063.691| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8892 Z= 0.327 Angle : 0.774 8.460 12162 Z= 0.377 Chirality : 0.047 0.280 1503 Planarity : 0.005 0.055 1494 Dihedral : 10.751 103.547 2100 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.97 % Allowed : 27.28 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 1054 helix: 1.29 (0.31), residues: 310 sheet: -1.47 (0.51), residues: 110 loop : -1.87 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 420 HIS 0.007 0.001 HIS B 595 PHE 0.023 0.001 PHE C 285 TYR 0.019 0.002 TYR B 709 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9355 (tmm) cc_final: 0.9132 (tmm) REVERT: D 528 TYR cc_start: 0.8566 (m-10) cc_final: 0.8200 (m-10) REVERT: D 634 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9113 (mmmm) REVERT: B 528 TYR cc_start: 0.8692 (m-10) cc_final: 0.8413 (m-10) REVERT: B 556 MET cc_start: 0.8690 (tmm) cc_final: 0.8423 (tmm) REVERT: B 634 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9101 (mmmm) REVERT: B 688 MET cc_start: 0.8516 (mtp) cc_final: 0.8290 (mtp) outliers start: 33 outliers final: 27 residues processed: 101 average time/residue: 0.1626 time to fit residues: 24.7248 Evaluate side-chains 98 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047492 restraints weight = 46121.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049207 restraints weight = 26422.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050379 restraints weight = 18653.176| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8892 Z= 0.268 Angle : 0.763 10.503 12162 Z= 0.369 Chirality : 0.048 0.279 1503 Planarity : 0.005 0.053 1494 Dihedral : 10.327 99.571 2100 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 4.21 % Allowed : 27.52 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.27), residues: 1054 helix: 1.22 (0.31), residues: 310 sheet: -1.65 (0.50), residues: 114 loop : -1.80 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 622 HIS 0.004 0.001 HIS A 222 PHE 0.010 0.001 PHE C 362 TYR 0.019 0.001 TYR B 709 ARG 0.002 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9346 (tmm) cc_final: 0.9107 (tmm) REVERT: D 525 LYS cc_start: 0.8039 (mttp) cc_final: 0.7620 (ptpp) REVERT: D 528 TYR cc_start: 0.8499 (m-10) cc_final: 0.8106 (m-10) REVERT: D 634 LYS cc_start: 0.9595 (mmtm) cc_final: 0.9108 (mmmm) REVERT: D 645 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8654 (mtp85) REVERT: A 280 MET cc_start: 0.9370 (tmm) cc_final: 0.8508 (mmt) REVERT: B 528 TYR cc_start: 0.8761 (m-10) cc_final: 0.8502 (m-10) REVERT: B 556 MET cc_start: 0.8715 (tmm) cc_final: 0.8083 (tmm) REVERT: B 622 TRP cc_start: 0.9530 (OUTLIER) cc_final: 0.8361 (t60) REVERT: B 634 LYS cc_start: 0.9610 (mmtm) cc_final: 0.9098 (mmmm) REVERT: B 688 MET cc_start: 0.8513 (mtp) cc_final: 0.8296 (mtp) outliers start: 35 outliers final: 30 residues processed: 103 average time/residue: 0.1826 time to fit residues: 27.3833 Evaluate side-chains 103 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047648 restraints weight = 46160.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049357 restraints weight = 26565.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050497 restraints weight = 18762.818| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8892 Z= 0.257 Angle : 0.761 10.238 12162 Z= 0.370 Chirality : 0.048 0.283 1503 Planarity : 0.005 0.053 1494 Dihedral : 9.795 93.218 2100 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 4.33 % Allowed : 27.16 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.27), residues: 1054 helix: 1.24 (0.31), residues: 310 sheet: -1.37 (0.56), residues: 100 loop : -1.83 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 622 HIS 0.004 0.001 HIS A 222 PHE 0.024 0.001 PHE C 285 TYR 0.018 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9346 (tmm) cc_final: 0.9099 (tmm) REVERT: D 405 MET cc_start: 0.8609 (tpp) cc_final: 0.7925 (ppp) REVERT: D 525 LYS cc_start: 0.8059 (mttp) cc_final: 0.7818 (mppt) REVERT: D 528 TYR cc_start: 0.8476 (m-10) cc_final: 0.8136 (m-10) REVERT: D 634 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9106 (mmmm) REVERT: A 280 MET cc_start: 0.9386 (tmm) cc_final: 0.8541 (mmt) REVERT: B 528 TYR cc_start: 0.8774 (m-10) cc_final: 0.8507 (m-10) REVERT: B 556 MET cc_start: 0.8734 (tmm) cc_final: 0.8029 (tmm) REVERT: B 622 TRP cc_start: 0.9527 (OUTLIER) cc_final: 0.8334 (t60) REVERT: B 634 LYS cc_start: 0.9609 (mmtm) cc_final: 0.9094 (mmmm) REVERT: B 688 MET cc_start: 0.8518 (mtp) cc_final: 0.8307 (mtp) outliers start: 36 outliers final: 32 residues processed: 102 average time/residue: 0.1827 time to fit residues: 27.4632 Evaluate side-chains 104 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 31 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048240 restraints weight = 44963.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049945 restraints weight = 25813.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051155 restraints weight = 18230.416| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8892 Z= 0.211 Angle : 0.753 9.892 12162 Z= 0.364 Chirality : 0.048 0.289 1503 Planarity : 0.005 0.055 1494 Dihedral : 9.264 87.387 2100 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 3.49 % Allowed : 28.25 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.27), residues: 1054 helix: 1.02 (0.31), residues: 320 sheet: -1.10 (0.57), residues: 96 loop : -1.74 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 608 HIS 0.003 0.001 HIS A 222 PHE 0.010 0.001 PHE C 362 TYR 0.018 0.001 TYR D 709 ARG 0.001 0.000 ARG D 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9340 (tmm) cc_final: 0.9089 (tmm) REVERT: D 405 MET cc_start: 0.8565 (tpp) cc_final: 0.7856 (ppp) REVERT: D 525 LYS cc_start: 0.8066 (mttp) cc_final: 0.7761 (ptpp) REVERT: D 528 TYR cc_start: 0.8453 (m-10) cc_final: 0.8103 (m-10) REVERT: D 634 LYS cc_start: 0.9604 (mmtm) cc_final: 0.9060 (mmmm) REVERT: A 280 MET cc_start: 0.9400 (tmm) cc_final: 0.8549 (mmt) REVERT: B 528 TYR cc_start: 0.8776 (m-10) cc_final: 0.8507 (m-10) REVERT: B 556 MET cc_start: 0.8732 (tmm) cc_final: 0.8019 (tmm) REVERT: B 622 TRP cc_start: 0.9533 (OUTLIER) cc_final: 0.8309 (t60) REVERT: B 634 LYS cc_start: 0.9612 (mmtm) cc_final: 0.9102 (mmmm) REVERT: B 688 MET cc_start: 0.8506 (mtp) cc_final: 0.8143 (mtp) outliers start: 29 outliers final: 28 residues processed: 97 average time/residue: 0.1804 time to fit residues: 25.7489 Evaluate side-chains 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048039 restraints weight = 45240.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049795 restraints weight = 25833.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050987 restraints weight = 18204.005| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8892 Z= 0.213 Angle : 0.749 9.749 12162 Z= 0.361 Chirality : 0.047 0.292 1503 Planarity : 0.005 0.055 1494 Dihedral : 8.692 78.808 2100 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.85 % Allowed : 28.25 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 1054 helix: 1.06 (0.31), residues: 320 sheet: -1.39 (0.51), residues: 118 loop : -1.77 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 622 HIS 0.003 0.001 HIS B 669 PHE 0.025 0.001 PHE C 285 TYR 0.015 0.001 TYR D 709 ARG 0.002 0.000 ARG D 665 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2685.74 seconds wall clock time: 49 minutes 9.89 seconds (2949.89 seconds total)