Starting phenix.real_space_refine on Mon May 12 06:20:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rjj_19243/05_2025/8rjj_19243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rjj_19243/05_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_19243/05_2025/8rjj_19243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rjj_19243/05_2025/8rjj_19243.map" model { file = "/net/cci-nas-00/data/ceres_data/8rjj_19243/05_2025/8rjj_19243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rjj_19243/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.14, per 1000 atoms: 0.71 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: 3.14 Conformation dependent library (CDL) restraints added in 1.0 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: 1.00 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: 2.28 Time building geometry restraints manager: 3.50 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: 1.430 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.180 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- 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 8955 Z= 0.255 Angle : 0.921 12.125 12321 Z= 0.437 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01270 ( 11) link_NAG-ASN : angle 3.94187 ( 33) link_BETA1-4 : bond 0.00579 ( 26) link_BETA1-4 : angle 2.35957 ( 78) hydrogen bonds : bond 0.14618 ( 283) hydrogen bonds : angle 6.33919 ( 795) SS BOND : bond 0.00324 ( 24) SS BOND : angle 1.02653 ( 48) covalent geometry : bond 0.00519 ( 8892) covalent geometry : angle 0.88194 (12162) Misc. bond : bond 0.00108 ( 2) *********************** 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 : 0.881 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: 0.1636 time to fit residues: 19.1027 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 : 0.840 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 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 = 0.047521 restraints weight = 46984.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049268 restraints weight = 27152.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050464 restraints weight = 19349.740| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 8955 Z= 0.194 Angle : 0.850 10.492 12321 Z= 0.393 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 11) link_NAG-ASN : angle 4.33002 ( 33) link_BETA1-4 : bond 0.00623 ( 26) link_BETA1-4 : angle 2.33846 ( 78) hydrogen bonds : bond 0.04492 ( 283) hydrogen bonds : angle 5.42568 ( 795) SS BOND : bond 0.00303 ( 24) SS BOND : angle 0.94388 ( 48) covalent geometry : bond 0.00411 ( 8892) covalent geometry : angle 0.80151 (12162) Misc. bond : bond 0.00079 ( 2) *********************** 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 : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9671 (tp) cc_final: 0.9459 (pp) REVERT: C 280 MET cc_start: 0.9349 (tmm) cc_final: 0.8656 (mmt) REVERT: D 634 LYS cc_start: 0.9591 (mmtm) cc_final: 0.9135 (mmmt) REVERT: B 447 PHE cc_start: 0.8230 (t80) cc_final: 0.8016 (t80) REVERT: B 530 TRP cc_start: 0.8144 (m100) cc_final: 0.7845 (m100) REVERT: B 634 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9095 (mmmm) outliers start: 42 outliers final: 19 residues processed: 112 average time/residue: 0.1505 time to fit residues: 25.9456 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 : 0.825 ------------------------------------------------------------------------------- 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: 50.0000 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 GLN ** 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 = 0.3460 r_free = 0.3460 target = 0.065589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048780 restraints weight = 46480.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050493 restraints weight = 26248.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051662 restraints weight = 18460.220| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8955 Z= 0.149 Angle : 0.827 10.995 12321 Z= 0.381 Chirality : 0.049 0.293 1503 Planarity : 0.005 0.050 1494 Dihedral : 14.655 114.691 2100 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 4.21 % Allowed : 23.68 % 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: -1.42 (0.27), residues: 1054 helix: 0.95 (0.30), residues: 322 sheet: -1.44 (0.51), residues: 92 loop : -1.99 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 530 HIS 0.003 0.001 HIS B 669 PHE 0.012 0.001 PHE D 510 TYR 0.020 0.001 TYR D 709 ARG 0.001 0.000 ARG D 665 Details of bonding type rmsd link_NAG-ASN : bond 0.01067 ( 11) link_NAG-ASN : angle 4.33718 ( 33) link_BETA1-4 : bond 0.00688 ( 26) link_BETA1-4 : angle 2.07783 ( 78) hydrogen bonds : bond 0.04045 ( 283) hydrogen bonds : angle 5.22312 ( 795) SS BOND : bond 0.00248 ( 24) SS BOND : angle 1.42399 ( 48) covalent geometry : bond 0.00312 ( 8892) covalent geometry : angle 0.77832 (12162) Misc. bond : bond 0.00075 ( 2) *********************** 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 116 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9653 (tp) cc_final: 0.9419 (pp) REVERT: C 280 MET cc_start: 0.9350 (tmm) cc_final: 0.9123 (tmm) REVERT: D 634 LYS cc_start: 0.9586 (mmtm) cc_final: 0.9114 (mmmt) REVERT: B 447 PHE cc_start: 0.8119 (t80) cc_final: 0.7909 (t80) REVERT: B 528 TYR cc_start: 0.8796 (m-10) cc_final: 0.8486 (m-10) REVERT: B 634 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9114 (mmmm) REVERT: B 688 MET cc_start: 0.8420 (mtp) cc_final: 0.8168 (mtp) outliers start: 35 outliers final: 17 residues processed: 109 average time/residue: 0.1544 time to fit residues: 25.4059 Evaluate side-chains 90 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 VAL 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 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 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: 0.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.065276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048554 restraints weight = 46087.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050258 restraints weight = 26326.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051376 restraints weight = 18653.183| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8955 Z= 0.162 Angle : 0.811 10.652 12321 Z= 0.377 Chirality : 0.048 0.304 1503 Planarity : 0.005 0.050 1494 Dihedral : 12.990 113.313 2100 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.49 % Allowed : 25.48 % Favored : 71.03 % 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: -1.29 (0.27), residues: 1054 helix: 1.06 (0.30), residues: 322 sheet: -1.39 (0.47), residues: 122 loop : -1.90 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 652 HIS 0.004 0.001 HIS B 595 PHE 0.023 0.001 PHE A 285 TYR 0.020 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 11) link_NAG-ASN : angle 4.25979 ( 33) link_BETA1-4 : bond 0.00621 ( 26) link_BETA1-4 : angle 2.06250 ( 78) hydrogen bonds : bond 0.03857 ( 283) hydrogen bonds : angle 5.19229 ( 795) SS BOND : bond 0.00293 ( 24) SS BOND : angle 1.32142 ( 48) covalent geometry : bond 0.00345 ( 8892) covalent geometry : angle 0.76297 (12162) Misc. bond : bond 0.00110 ( 2) *********************** 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 103 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9667 (tp) cc_final: 0.9421 (pp) REVERT: C 280 MET cc_start: 0.9362 (tmm) cc_final: 0.9111 (tmm) REVERT: D 528 TYR cc_start: 0.8549 (m-10) cc_final: 0.8221 (m-10) REVERT: D 634 LYS cc_start: 0.9587 (mmtm) cc_final: 0.9149 (mmmt) REVERT: B 528 TYR cc_start: 0.8766 (m-10) cc_final: 0.8405 (m-10) REVERT: B 634 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9107 (mmmm) REVERT: B 688 MET cc_start: 0.8429 (mtp) cc_final: 0.8169 (ttm) outliers start: 29 outliers final: 20 residues processed: 96 average time/residue: 0.1619 time to fit residues: 23.5947 Evaluate side-chains 91 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 40 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 78 optimal weight: 0.0020 chunk 79 optimal weight: 2.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- 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** A 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048355 restraints weight = 46340.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050054 restraints weight = 26445.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051229 restraints weight = 18683.366| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8955 Z= 0.162 Angle : 0.787 10.293 12321 Z= 0.369 Chirality : 0.047 0.291 1503 Planarity : 0.005 0.051 1494 Dihedral : 11.884 111.357 2100 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 4.33 % Allowed : 24.76 % Favored : 70.91 % 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: -1.26 (0.27), residues: 1054 helix: 1.10 (0.31), residues: 322 sheet: -1.46 (0.47), residues: 122 loop : -1.88 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 652 HIS 0.004 0.001 HIS B 595 PHE 0.023 0.001 PHE A 285 TYR 0.020 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 11) link_NAG-ASN : angle 4.12379 ( 33) link_BETA1-4 : bond 0.00624 ( 26) link_BETA1-4 : angle 1.96852 ( 78) hydrogen bonds : bond 0.03759 ( 283) hydrogen bonds : angle 5.16452 ( 795) SS BOND : bond 0.00249 ( 24) SS BOND : angle 1.18089 ( 48) covalent geometry : bond 0.00345 ( 8892) covalent geometry : angle 0.74232 (12162) Misc. bond : bond 0.00076 ( 2) *********************** 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 111 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9671 (tp) cc_final: 0.9424 (pp) REVERT: D 525 LYS cc_start: 0.8025 (mttp) cc_final: 0.7816 (mppt) REVERT: D 528 TYR cc_start: 0.8543 (m-10) cc_final: 0.8216 (m-10) REVERT: D 634 LYS cc_start: 0.9591 (mmtm) cc_final: 0.9113 (mmmm) REVERT: A 280 MET cc_start: 0.9351 (tmm) cc_final: 0.8456 (mmt) REVERT: B 528 TYR cc_start: 0.8735 (m-10) cc_final: 0.8336 (m-10) REVERT: B 634 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9112 (mmmm) REVERT: B 688 MET cc_start: 0.8457 (mtp) cc_final: 0.8203 (mtp) outliers start: 36 outliers final: 24 residues processed: 104 average time/residue: 0.1676 time to fit residues: 26.1838 Evaluate side-chains 96 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 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 520 THR Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 32 optimal weight: 0.0030 chunk 102 optimal weight: 0.9980 overall best weight: 1.8594 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.065519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048733 restraints weight = 45713.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050427 restraints weight = 26219.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051577 restraints weight = 18579.958| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8955 Z= 0.154 Angle : 0.792 9.908 12321 Z= 0.373 Chirality : 0.047 0.291 1503 Planarity : 0.005 0.052 1494 Dihedral : 11.410 109.456 2100 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.33 % Allowed : 25.24 % Favored : 70.43 % 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: -1.26 (0.27), residues: 1054 helix: 1.03 (0.31), residues: 322 sheet: -1.44 (0.47), residues: 122 loop : -1.83 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 652 HIS 0.003 0.001 HIS B 595 PHE 0.024 0.001 PHE A 285 TYR 0.020 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 11) link_NAG-ASN : angle 4.08462 ( 33) link_BETA1-4 : bond 0.00627 ( 26) link_BETA1-4 : angle 1.92916 ( 78) hydrogen bonds : bond 0.03777 ( 283) hydrogen bonds : angle 5.22423 ( 795) SS BOND : bond 0.00248 ( 24) SS BOND : angle 1.20446 ( 48) covalent geometry : bond 0.00334 ( 8892) covalent geometry : angle 0.74872 (12162) Misc. bond : bond 0.00079 ( 2) *********************** 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 112 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 525 LYS cc_start: 0.8064 (mttp) cc_final: 0.7840 (mppt) REVERT: D 528 TYR cc_start: 0.8503 (m-10) cc_final: 0.8168 (m-10) REVERT: D 634 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9117 (mmmm) REVERT: A 280 MET cc_start: 0.9363 (tmm) cc_final: 0.8442 (mmt) REVERT: B 528 TYR cc_start: 0.8706 (m-10) cc_final: 0.8448 (m-10) REVERT: B 634 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9102 (mmmm) REVERT: B 688 MET cc_start: 0.8452 (mtp) cc_final: 0.8240 (mtp) outliers start: 36 outliers final: 29 residues processed: 106 average time/residue: 0.1548 time to fit residues: 24.8722 Evaluate side-chains 102 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 520 THR Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 chunk 64 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047115 restraints weight = 46264.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048789 restraints weight = 26893.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049919 restraints weight = 19134.465| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8955 Z= 0.223 Angle : 0.811 9.058 12321 Z= 0.384 Chirality : 0.048 0.280 1503 Planarity : 0.005 0.053 1494 Dihedral : 10.887 104.628 2100 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 4.21 % Allowed : 26.20 % Favored : 69.59 % 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: -1.27 (0.27), residues: 1054 helix: 1.05 (0.31), residues: 322 sheet: -1.34 (0.51), residues: 108 loop : -1.89 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 622 HIS 0.006 0.001 HIS B 595 PHE 0.025 0.002 PHE C 285 TYR 0.018 0.002 TYR D 709 ARG 0.003 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 11) link_NAG-ASN : angle 3.88914 ( 33) link_BETA1-4 : bond 0.00587 ( 26) link_BETA1-4 : angle 2.05952 ( 78) hydrogen bonds : bond 0.04032 ( 283) hydrogen bonds : angle 5.28539 ( 795) SS BOND : bond 0.00331 ( 24) SS BOND : angle 1.23875 ( 48) covalent geometry : bond 0.00480 ( 8892) covalent geometry : angle 0.76961 (12162) Misc. bond : bond 0.00063 ( 2) *********************** 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 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9347 (tmm) cc_final: 0.9117 (tmm) REVERT: D 528 TYR cc_start: 0.8513 (m-10) cc_final: 0.8186 (m-10) REVERT: D 634 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9112 (mmmm) REVERT: A 280 MET cc_start: 0.9403 (tmm) cc_final: 0.8505 (mmt) REVERT: B 528 TYR cc_start: 0.8696 (m-10) cc_final: 0.8432 (m-10) REVERT: B 556 MET cc_start: 0.8685 (tmm) cc_final: 0.8399 (tmm) REVERT: B 634 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9124 (mmmm) REVERT: B 688 MET cc_start: 0.8535 (mtp) cc_final: 0.8302 (mtp) outliers start: 35 outliers final: 28 residues processed: 102 average time/residue: 0.1584 time to fit residues: 24.2872 Evaluate side-chains 98 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 520 THR Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL 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: 8.9990 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.065190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048418 restraints weight = 46798.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050136 restraints weight = 26683.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051289 restraints weight = 18758.182| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8955 Z= 0.154 Angle : 0.785 9.632 12321 Z= 0.370 Chirality : 0.048 0.290 1503 Planarity : 0.005 0.052 1494 Dihedral : 10.458 101.591 2100 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 3.85 % Allowed : 26.68 % Favored : 69.47 % 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: -1.25 (0.27), residues: 1054 helix: 1.03 (0.31), residues: 322 sheet: -1.33 (0.51), residues: 108 loop : -1.84 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 622 HIS 0.003 0.001 HIS A 222 PHE 0.023 0.001 PHE A 285 TYR 0.019 0.001 TYR D 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 11) link_NAG-ASN : angle 3.78485 ( 33) link_BETA1-4 : bond 0.00649 ( 26) link_BETA1-4 : angle 1.90453 ( 78) hydrogen bonds : bond 0.03791 ( 283) hydrogen bonds : angle 5.24093 ( 795) SS BOND : bond 0.00219 ( 24) SS BOND : angle 1.10386 ( 48) covalent geometry : bond 0.00333 ( 8892) covalent geometry : angle 0.74702 (12162) Misc. bond : bond 0.00062 ( 2) *********************** 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 105 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9339 (tmm) cc_final: 0.9090 (tmm) REVERT: D 528 TYR cc_start: 0.8499 (m-10) cc_final: 0.8158 (m-10) REVERT: D 634 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9072 (mmmm) REVERT: B 528 TYR cc_start: 0.8702 (m-10) cc_final: 0.8435 (m-10) REVERT: B 556 MET cc_start: 0.8701 (tmm) cc_final: 0.8486 (tmm) REVERT: B 634 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9118 (mmmm) REVERT: B 688 MET cc_start: 0.8479 (mtp) cc_final: 0.8260 (mtp) outliers start: 32 outliers final: 26 residues processed: 99 average time/residue: 0.1703 time to fit residues: 25.2242 Evaluate side-chains 96 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 212 ILE 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 520 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL 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: 0.5980 chunk 61 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.064861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047619 restraints weight = 45406.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049300 restraints weight = 26215.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050453 restraints weight = 18672.278| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8955 Z= 0.176 Angle : 0.794 10.506 12321 Z= 0.375 Chirality : 0.048 0.295 1503 Planarity : 0.005 0.057 1494 Dihedral : 9.877 94.691 2100 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.49 % Allowed : 26.80 % Favored : 69.71 % 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: 1.04 (0.31), residues: 322 sheet: -1.12 (0.57), residues: 96 loop : -1.82 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 622 HIS 0.004 0.001 HIS A 222 PHE 0.030 0.002 PHE A 285 TYR 0.018 0.001 TYR B 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 11) link_NAG-ASN : angle 3.67225 ( 33) link_BETA1-4 : bond 0.00604 ( 26) link_BETA1-4 : angle 1.99520 ( 78) hydrogen bonds : bond 0.03850 ( 283) hydrogen bonds : angle 5.26997 ( 795) SS BOND : bond 0.00258 ( 24) SS BOND : angle 1.10610 ( 48) covalent geometry : bond 0.00381 ( 8892) covalent geometry : angle 0.75611 (12162) Misc. bond : bond 0.00066 ( 2) *********************** 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 101 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9351 (tmm) cc_final: 0.9099 (tmm) REVERT: D 525 LYS cc_start: 0.8467 (mppt) cc_final: 0.8242 (ptpp) REVERT: D 528 TYR cc_start: 0.8478 (m-10) cc_final: 0.8125 (m-10) REVERT: D 634 LYS cc_start: 0.9553 (mmtm) cc_final: 0.9104 (mmmm) REVERT: D 668 GLN cc_start: 0.9098 (mt0) cc_final: 0.8775 (mt0) REVERT: A 280 MET cc_start: 0.9384 (tmm) cc_final: 0.8517 (mmt) REVERT: B 528 TYR cc_start: 0.8754 (m-10) cc_final: 0.8493 (m-10) REVERT: B 556 MET cc_start: 0.8718 (tmm) cc_final: 0.8467 (tmm) REVERT: B 634 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9119 (mmmm) REVERT: B 688 MET cc_start: 0.8524 (mtp) cc_final: 0.8307 (mtp) outliers start: 29 outliers final: 26 residues processed: 97 average time/residue: 0.1615 time to fit residues: 23.4995 Evaluate side-chains 97 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL 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: 2.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 19 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.064350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047180 restraints weight = 45809.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048863 restraints weight = 26573.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050019 restraints weight = 18936.060| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8955 Z= 0.205 Angle : 0.813 10.638 12321 Z= 0.383 Chirality : 0.048 0.291 1503 Planarity : 0.005 0.054 1494 Dihedral : 9.476 87.814 2100 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.37 % Allowed : 27.04 % Favored : 69.59 % 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: -1.24 (0.27), residues: 1054 helix: 1.00 (0.31), residues: 322 sheet: -1.13 (0.57), residues: 96 loop : -1.85 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 622 HIS 0.010 0.001 HIS D 669 PHE 0.012 0.001 PHE C 362 TYR 0.017 0.001 TYR B 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 11) link_NAG-ASN : angle 3.63986 ( 33) link_BETA1-4 : bond 0.00578 ( 26) link_BETA1-4 : angle 2.05163 ( 78) hydrogen bonds : bond 0.03929 ( 283) hydrogen bonds : angle 5.35499 ( 795) SS BOND : bond 0.00301 ( 24) SS BOND : angle 1.15342 ( 48) covalent geometry : bond 0.00442 ( 8892) covalent geometry : angle 0.77536 (12162) Misc. bond : bond 0.00075 ( 2) ********************** 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 98 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9343 (tmm) cc_final: 0.9090 (tmm) REVERT: D 525 LYS cc_start: 0.8566 (mppt) cc_final: 0.8353 (pttm) REVERT: D 528 TYR cc_start: 0.8477 (m-10) cc_final: 0.8075 (m-10) REVERT: D 634 LYS cc_start: 0.9578 (mmtm) cc_final: 0.9116 (mmmm) REVERT: D 668 GLN cc_start: 0.9132 (mt0) cc_final: 0.8838 (mm110) REVERT: A 280 MET cc_start: 0.9375 (tmm) cc_final: 0.8527 (mmt) REVERT: B 528 TYR cc_start: 0.8793 (m-10) cc_final: 0.8524 (m-10) REVERT: B 556 MET cc_start: 0.8734 (tmm) cc_final: 0.8471 (tmm) REVERT: B 634 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9118 (mmmm) REVERT: B 688 MET cc_start: 0.8544 (mtp) cc_final: 0.8334 (mtp) outliers start: 28 outliers final: 27 residues processed: 93 average time/residue: 0.1836 time to fit residues: 25.1542 Evaluate side-chains 97 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 212 ILE 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 628 VAL 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: 1.9990 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.064664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047558 restraints weight = 45530.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049265 restraints weight = 26182.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050423 restraints weight = 18486.807| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8955 Z= 0.178 Angle : 0.802 10.345 12321 Z= 0.377 Chirality : 0.048 0.294 1503 Planarity : 0.005 0.054 1494 Dihedral : 8.940 79.965 2100 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.61 % Allowed : 27.04 % Favored : 69.35 % 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: -1.23 (0.27), residues: 1054 helix: 0.96 (0.30), residues: 322 sheet: -1.08 (0.57), residues: 96 loop : -1.82 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 622 HIS 0.004 0.001 HIS A 222 PHE 0.025 0.001 PHE C 285 TYR 0.015 0.001 TYR B 709 ARG 0.001 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 11) link_NAG-ASN : angle 3.56046 ( 33) link_BETA1-4 : bond 0.00592 ( 26) link_BETA1-4 : angle 2.05724 ( 78) hydrogen bonds : bond 0.03832 ( 283) hydrogen bonds : angle 5.28298 ( 795) SS BOND : bond 0.00268 ( 24) SS BOND : angle 1.11704 ( 48) covalent geometry : bond 0.00385 ( 8892) covalent geometry : angle 0.76524 (12162) Misc. bond : bond 0.00074 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.81 seconds wall clock time: 46 minutes 7.19 seconds (2767.19 seconds total)