Starting phenix.real_space_refine on Tue Apr 29 16:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rjj_19243/04_2025/8rjj_19243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rjj_19243/04_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_19243/04_2025/8rjj_19243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rjj_19243/04_2025/8rjj_19243.map" model { file = "/net/cci-nas-00/data/ceres_data/8rjj_19243/04_2025/8rjj_19243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rjj_19243/04_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-5669/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: 6.04, per 1000 atoms: 0.70 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: 3.04 Conformation dependent library (CDL) restraints added in 971.3 milliseconds 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: 0.86 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: 2.24 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2683 1.34 - 1.46: 2080 1.46 - 1.58: 4045 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8892 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C1 BMA S 3 " pdb=" O5 BMA S 3 " ideal model delta sigma weight residual 1.410 1.450 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sigma weight residual 1.410 1.450 -0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 8887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 11839 2.43 - 4.85: 257 4.85 - 7.27: 59 7.27 - 9.70: 6 9.70 - 12.12: 1 Bond angle restraints: 12162 Sorted by residual: angle pdb=" N PRO C 326 " pdb=" CA PRO C 326 " pdb=" CB PRO C 326 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.68e+01 angle pdb=" N PRO A 326 " pdb=" CA PRO A 326 " pdb=" CB PRO A 326 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" CB MET C 280 " pdb=" CG MET C 280 " pdb=" SD MET C 280 " ideal model delta sigma weight residual 112.70 124.82 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C TYR C 361 " pdb=" N PHE C 362 " pdb=" CA PHE C 362 " ideal model delta sigma weight residual 121.66 115.22 6.44 1.76e+00 3.23e-01 1.34e+01 angle pdb=" CB LYS B 634 " pdb=" CG LYS B 634 " pdb=" CD LYS B 634 " ideal model delta sigma weight residual 111.30 119.63 -8.33 2.30e+00 1.89e-01 1.31e+01 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.80: 5261 25.80 - 51.60: 378 51.60 - 77.39: 80 77.39 - 103.19: 52 103.19 - 128.99: 33 Dihedral angle restraints: 5804 sinusoidal: 2708 harmonic: 3096 Sorted by residual: dihedral pdb=" CA PHE B 510 " pdb=" C PHE B 510 " pdb=" N THR B 511 " pdb=" CA THR B 511 " ideal model delta harmonic sigma weight residual 180.00 142.36 37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CB CYS D 452 " pdb=" SG CYS D 452 " pdb=" SG CYS D 626 " pdb=" CB CYS D 626 " ideal model delta sinusoidal sigma weight residual 93.00 153.93 -60.93 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS C 272 " pdb=" SG CYS C 272 " pdb=" SG CYS C 281 " pdb=" CB CYS C 281 " ideal model delta sinusoidal sigma weight residual 93.00 153.46 -60.46 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1432 0.105 - 0.209: 55 0.209 - 0.314: 14 0.314 - 0.419: 1 0.419 - 0.523: 1 Chirality restraints: 1503 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 305 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN D 629 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C4 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C5 NAG K 1 " pdb=" O4 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1500 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 305 " -0.024 2.00e-02 2.50e+03 2.30e-02 6.60e+00 pdb=" CG ASN C 305 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 305 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 305 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 525 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 526 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 557 " 0.019 2.00e-02 2.50e+03 1.70e-02 3.59e+00 pdb=" CG ASN B 557 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 557 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 557 " -0.017 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.019 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 283 2.65 - 3.21: 9241 3.21 - 3.77: 14473 3.77 - 4.34: 17954 4.34 - 4.90: 27475 Nonbonded interactions: 69426 Sorted by model distance: nonbonded pdb=" O GLN D 409 " pdb=" OH TYR D 443 " model vdw 2.086 3.040 nonbonded pdb=" OD1 ASP C 232 " pdb=" OG1 THR C 235 " model vdw 2.113 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" OG1 THR A 235 " model vdw 2.117 3.040 nonbonded pdb=" O GLN B 409 " pdb=" OH TYR B 443 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASN D 423 " pdb=" OG1 THR D 425 " model vdw 2.176 3.040 ... (remaining 69421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.750 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- 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 : 1.034 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: 0.1682 time to fit residues: 19.6803 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 : 0.902 ------------------------------------------------------------------------------- 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 = 0.047514 restraints weight = 46984.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049279 restraints weight = 27164.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050455 restraints weight = 19359.117| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 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 : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9671 (tp) cc_final: 0.9458 (pp) REVERT: C 280 MET cc_start: 0.9349 (tmm) cc_final: 0.8655 (mmt) REVERT: D 634 LYS cc_start: 0.9590 (mmtm) cc_final: 0.9135 (mmmt) REVERT: B 447 PHE cc_start: 0.8231 (t80) cc_final: 0.8017 (t80) REVERT: B 530 TRP cc_start: 0.8144 (m100) cc_final: 0.7846 (m100) REVERT: B 634 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9095 (mmmm) outliers start: 42 outliers final: 19 residues processed: 112 average time/residue: 0.1674 time to fit residues: 29.1990 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 : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN C 222 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048043 restraints weight = 47195.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049685 restraints weight = 26876.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050866 restraints weight = 18969.549| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1297 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= 0.186 Angle : 0.828 10.560 12321 Z= 0.385 Chirality : 0.049 0.305 1503 Planarity : 0.005 0.051 1494 Dihedral : 14.307 114.656 2100 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 5.05 % Allowed : 22.60 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 1054 helix: 1.16 (0.31), residues: 310 sheet: -1.43 (0.50), residues: 104 loop : -2.05 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 530 HIS 0.005 0.001 HIS C 222 PHE 0.012 0.001 PHE D 510 TYR 0.020 0.002 TYR D 709 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 11) link_NAG-ASN : angle 4.25805 ( 33) link_BETA1-4 : bond 0.00621 ( 26) link_BETA1-4 : angle 2.07956 ( 78) hydrogen bonds : bond 0.04193 ( 283) hydrogen bonds : angle 5.26649 ( 795) SS BOND : bond 0.00303 ( 24) SS BOND : angle 1.46919 ( 48) covalent geometry : bond 0.00397 ( 8892) covalent geometry : angle 0.78087 (12162) Misc. bond : bond 0.00061 ( 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 122 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9655 (tp) cc_final: 0.9418 (pp) REVERT: C 280 MET cc_start: 0.9357 (tmm) cc_final: 0.9135 (tmm) REVERT: D 634 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9149 (mmmt) REVERT: B 447 PHE cc_start: 0.8221 (t80) cc_final: 0.7975 (t80) REVERT: B 528 TYR cc_start: 0.8806 (m-10) cc_final: 0.8473 (m-10) REVERT: B 634 LYS cc_start: 0.9600 (mmtm) cc_final: 0.9116 (mmmm) REVERT: B 688 MET cc_start: 0.8476 (mtp) cc_final: 0.8231 (mtp) outliers start: 42 outliers final: 24 residues processed: 112 average time/residue: 0.1775 time to fit residues: 30.1699 Evaluate side-chains 95 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU 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 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 50.0000 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 GLN A 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.064962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048236 restraints weight = 45885.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049917 restraints weight = 26311.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051052 restraints weight = 18643.201| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8955 Z= 0.165 Angle : 0.814 10.660 12321 Z= 0.381 Chirality : 0.048 0.303 1503 Planarity : 0.005 0.053 1494 Dihedral : 12.988 112.964 2100 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 3.61 % Allowed : 25.48 % 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: -1.35 (0.27), residues: 1054 helix: 1.21 (0.31), residues: 310 sheet: -1.54 (0.47), residues: 124 loop : -1.98 (0.25), residues: 620 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 0.021 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 0.00784 ( 11) link_NAG-ASN : angle 4.25041 ( 33) link_BETA1-4 : bond 0.00607 ( 26) link_BETA1-4 : angle 2.03486 ( 78) hydrogen bonds : bond 0.03883 ( 283) hydrogen bonds : angle 5.22620 ( 795) SS BOND : bond 0.00239 ( 24) SS BOND : angle 1.43210 ( 48) covalent geometry : bond 0.00351 ( 8892) covalent geometry : angle 0.76688 (12162) Misc. bond : bond 0.00103 ( 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: 30 poor density : 73 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9674 (tp) cc_final: 0.9421 (pp) REVERT: C 280 MET cc_start: 0.9363 (tmm) cc_final: 0.9121 (tmm) REVERT: D 634 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9149 (mmmt) REVERT: B 528 TYR cc_start: 0.8758 (m-10) cc_final: 0.8364 (m-10) REVERT: B 634 LYS cc_start: 0.9598 (mmtm) cc_final: 0.9110 (mmmm) REVERT: B 688 MET cc_start: 0.8457 (mtp) cc_final: 0.8196 (mtp) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 0.2564 time to fit residues: 37.3484 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 : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 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 372 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 78 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.064076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047246 restraints weight = 45819.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048909 restraints weight = 26506.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050052 restraints weight = 18812.923| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8955 Z= 0.220 Angle : 0.808 9.987 12321 Z= 0.382 Chirality : 0.048 0.301 1503 Planarity : 0.005 0.055 1494 Dihedral : 12.096 110.894 2100 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.81 % Allowed : 24.40 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 1054 helix: 1.25 (0.31), residues: 310 sheet: -1.64 (0.47), residues: 124 loop : -1.91 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 420 HIS 0.005 0.001 HIS A 222 PHE 0.010 0.001 PHE B 510 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 0.00581 ( 11) link_NAG-ASN : angle 4.13516 ( 33) link_BETA1-4 : bond 0.00578 ( 26) link_BETA1-4 : angle 2.05699 ( 78) hydrogen bonds : bond 0.03927 ( 283) hydrogen bonds : angle 5.30792 ( 795) SS BOND : bond 0.00341 ( 24) SS BOND : angle 1.30035 ( 48) covalent geometry : bond 0.00473 ( 8892) covalent geometry : angle 0.76202 (12162) Misc. bond : bond 0.00061 ( 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: 40 poor density : 71 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9663 (tp) cc_final: 0.9419 (pp) REVERT: D 528 TYR cc_start: 0.8530 (m-10) cc_final: 0.8197 (m-10) REVERT: D 634 LYS cc_start: 0.9598 (mmtm) cc_final: 0.9117 (mmmm) REVERT: B 528 TYR cc_start: 0.8727 (m-10) cc_final: 0.8479 (m-10) REVERT: B 634 LYS cc_start: 0.9597 (mmtm) cc_final: 0.9106 (mmmm) REVERT: B 688 MET cc_start: 0.8501 (mtp) cc_final: 0.8255 (mtp) outliers start: 40 outliers final: 27 residues processed: 105 average time/residue: 0.1672 time to fit residues: 26.9624 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 : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 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 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 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 Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.065000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048267 restraints weight = 45765.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049938 restraints weight = 26343.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051075 restraints weight = 18710.079| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8955 Z= 0.162 Angle : 0.798 9.814 12321 Z= 0.376 Chirality : 0.048 0.286 1503 Planarity : 0.005 0.054 1494 Dihedral : 11.511 108.743 2100 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 4.21 % Allowed : 25.48 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 1054 helix: 1.13 (0.31), residues: 310 sheet: -1.59 (0.47), residues: 124 loop : -1.88 (0.26), residues: 620 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 0.056 0.002 PHE A 345 TYR 0.020 0.001 TYR B 709 ARG 0.002 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 11) link_NAG-ASN : angle 4.00755 ( 33) link_BETA1-4 : bond 0.00628 ( 26) link_BETA1-4 : angle 1.93890 ( 78) hydrogen bonds : bond 0.03886 ( 283) hydrogen bonds : angle 5.28031 ( 795) SS BOND : bond 0.00241 ( 24) SS BOND : angle 1.18699 ( 48) covalent geometry : bond 0.00349 ( 8892) covalent geometry : angle 0.75655 (12162) Misc. bond : bond 0.00076 ( 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 110 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 528 TYR cc_start: 0.8529 (m-10) cc_final: 0.8201 (m-10) REVERT: D 634 LYS cc_start: 0.9601 (mmtm) cc_final: 0.9112 (mmmm) REVERT: B 528 TYR cc_start: 0.8729 (m-10) cc_final: 0.8469 (m-10) REVERT: B 634 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9100 (mmmm) REVERT: B 688 MET cc_start: 0.8487 (mtp) cc_final: 0.8244 (mtp) outliers start: 35 outliers final: 29 residues processed: 101 average time/residue: 0.1658 time to fit residues: 25.1045 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 : 0.984 ------------------------------------------------------------------------------- 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 373 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS 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 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 Chi-restraints excluded: chain B residue 638 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 0.0270 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 50.0000 chunk 64 optimal weight: 6.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.064911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047664 restraints weight = 45502.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049344 restraints weight = 26164.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050509 restraints weight = 18549.892| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8955 Z= 0.174 Angle : 0.793 10.498 12321 Z= 0.374 Chirality : 0.048 0.285 1503 Planarity : 0.005 0.055 1494 Dihedral : 10.846 104.265 2100 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 4.57 % Allowed : 26.08 % 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: -1.30 (0.27), residues: 1054 helix: 1.18 (0.31), residues: 310 sheet: -1.59 (0.47), residues: 124 loop : -1.87 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 622 HIS 0.007 0.001 HIS B 595 PHE 0.045 0.001 PHE A 345 TYR 0.019 0.001 TYR D 709 ARG 0.001 0.000 ARG B 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 11) link_NAG-ASN : angle 3.80246 ( 33) link_BETA1-4 : bond 0.00622 ( 26) link_BETA1-4 : angle 1.94793 ( 78) hydrogen bonds : bond 0.03908 ( 283) hydrogen bonds : angle 5.25514 ( 795) SS BOND : bond 0.00256 ( 24) SS BOND : angle 1.17825 ( 48) covalent geometry : bond 0.00376 ( 8892) covalent geometry : angle 0.75372 (12162) Misc. bond : bond 0.00080 ( 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 111 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9350 (tmm) cc_final: 0.9123 (tmm) REVERT: D 528 TYR cc_start: 0.8549 (m-10) cc_final: 0.8222 (m-10) REVERT: D 634 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9104 (mmmm) REVERT: A 280 MET cc_start: 0.9372 (tmm) cc_final: 0.8531 (mmt) REVERT: B 528 TYR cc_start: 0.8721 (m-10) cc_final: 0.8453 (m-10) REVERT: B 556 MET cc_start: 0.8714 (tmm) cc_final: 0.8460 (tmm) REVERT: B 634 LYS cc_start: 0.9608 (mmtm) cc_final: 0.9108 (mmmm) REVERT: B 688 MET cc_start: 0.8505 (mtp) cc_final: 0.8277 (mtp) outliers start: 38 outliers final: 31 residues processed: 104 average time/residue: 0.1642 time to fit residues: 25.8512 Evaluate side-chains 102 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 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 591 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 0.0170 chunk 28 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 65 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.065374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048493 restraints weight = 46671.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050159 restraints weight = 26805.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051340 restraints weight = 18863.715| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2127 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= 0.144 Angle : 0.777 9.859 12321 Z= 0.366 Chirality : 0.047 0.289 1503 Planarity : 0.005 0.055 1494 Dihedral : 10.295 100.074 2100 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.97 % Allowed : 26.92 % Favored : 69.11 % 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: -1.25 (0.27), residues: 1054 helix: 1.23 (0.31), residues: 310 sheet: -1.52 (0.51), residues: 122 loop : -1.85 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 622 HIS 0.003 0.001 HIS A 222 PHE 0.039 0.001 PHE A 345 TYR 0.020 0.001 TYR B 709 ARG 0.001 0.000 ARG B 636 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 11) link_NAG-ASN : angle 3.71236 ( 33) link_BETA1-4 : bond 0.00652 ( 26) link_BETA1-4 : angle 1.89088 ( 78) hydrogen bonds : bond 0.03767 ( 283) hydrogen bonds : angle 5.19733 ( 795) SS BOND : bond 0.00222 ( 24) SS BOND : angle 1.09395 ( 48) covalent geometry : bond 0.00309 ( 8892) covalent geometry : angle 0.73914 (12162) Misc. bond : bond 0.00084 ( 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 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9343 (tmm) cc_final: 0.9092 (tmm) REVERT: D 525 LYS cc_start: 0.8028 (mttp) cc_final: 0.7643 (ptpp) REVERT: D 528 TYR cc_start: 0.8471 (m-10) cc_final: 0.8120 (m-10) REVERT: D 634 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9063 (mmmm) REVERT: A 280 MET cc_start: 0.9366 (tmm) cc_final: 0.8465 (mmt) REVERT: B 528 TYR cc_start: 0.8757 (m-10) cc_final: 0.8496 (m-10) REVERT: B 556 MET cc_start: 0.8688 (tmm) cc_final: 0.8476 (tmm) REVERT: B 634 LYS cc_start: 0.9611 (mmtm) cc_final: 0.9113 (mmmm) outliers start: 33 outliers final: 33 residues processed: 103 average time/residue: 0.1796 time to fit residues: 27.1125 Evaluate side-chains 104 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 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 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 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 40.0000 chunk 89 optimal weight: 0.0770 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.3556 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048837 restraints weight = 45550.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050555 restraints weight = 25877.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051699 restraints weight = 18230.813| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8955 Z= 0.137 Angle : 0.776 9.859 12321 Z= 0.365 Chirality : 0.047 0.291 1503 Planarity : 0.005 0.053 1494 Dihedral : 9.556 92.674 2100 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 3.97 % Allowed : 26.92 % Favored : 69.11 % 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: -1.16 (0.27), residues: 1054 helix: 0.95 (0.30), residues: 334 sheet: -1.28 (0.52), residues: 118 loop : -1.75 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 622 HIS 0.003 0.001 HIS D 669 PHE 0.037 0.001 PHE A 345 TYR 0.019 0.001 TYR B 709 ARG 0.002 0.000 ARG B 636 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 11) link_NAG-ASN : angle 3.58658 ( 33) link_BETA1-4 : bond 0.00650 ( 26) link_BETA1-4 : angle 1.91245 ( 78) hydrogen bonds : bond 0.03665 ( 283) hydrogen bonds : angle 5.13679 ( 795) SS BOND : bond 0.00198 ( 24) SS BOND : angle 1.06752 ( 48) covalent geometry : bond 0.00292 ( 8892) covalent geometry : angle 0.73971 (12162) Misc. bond : bond 0.00087 ( 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 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9337 (tmm) cc_final: 0.9074 (tmm) REVERT: D 405 MET cc_start: 0.8484 (tpp) cc_final: 0.7784 (ppp) REVERT: D 525 LYS cc_start: 0.8014 (mttp) cc_final: 0.7686 (ptpp) REVERT: D 528 TYR cc_start: 0.8440 (m-10) cc_final: 0.8096 (m-10) REVERT: D 634 LYS cc_start: 0.9541 (mmtm) cc_final: 0.9090 (mmmm) REVERT: A 280 MET cc_start: 0.9377 (tmm) cc_final: 0.8490 (mmt) REVERT: B 528 TYR cc_start: 0.8759 (m-10) cc_final: 0.8527 (m-10) REVERT: B 556 MET cc_start: 0.8670 (tmm) cc_final: 0.8015 (tmm) REVERT: B 622 TRP cc_start: 0.9480 (OUTLIER) cc_final: 0.8272 (t60) REVERT: B 634 LYS cc_start: 0.9605 (mmtm) cc_final: 0.9107 (mmmm) outliers start: 33 outliers final: 29 residues processed: 103 average time/residue: 0.1749 time to fit residues: 26.5367 Evaluate side-chains 102 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 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 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 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.064541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047741 restraints weight = 46489.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049406 restraints weight = 26747.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050513 restraints weight = 18963.074| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8955 Z= 0.195 Angle : 0.798 9.420 12321 Z= 0.375 Chirality : 0.047 0.291 1503 Planarity : 0.005 0.052 1494 Dihedral : 9.204 85.080 2100 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 3.61 % Allowed : 27.52 % Favored : 68.87 % 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: -1.13 (0.27), residues: 1054 helix: 1.06 (0.31), residues: 322 sheet: -0.98 (0.57), residues: 96 loop : -1.79 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 420 HIS 0.004 0.001 HIS A 222 PHE 0.039 0.002 PHE A 345 TYR 0.017 0.001 TYR B 709 ARG 0.002 0.000 ARG B 593 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 11) link_NAG-ASN : angle 3.54786 ( 33) link_BETA1-4 : bond 0.00577 ( 26) link_BETA1-4 : angle 2.08320 ( 78) hydrogen bonds : bond 0.03840 ( 283) hydrogen bonds : angle 5.25506 ( 795) SS BOND : bond 0.00287 ( 24) SS BOND : angle 1.16030 ( 48) covalent geometry : bond 0.00421 ( 8892) covalent geometry : angle 0.76040 (12162) Misc. bond : bond 0.00059 ( 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 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 MET cc_start: 0.9341 (tmm) cc_final: 0.9076 (tmm) REVERT: D 525 LYS cc_start: 0.8077 (mttp) cc_final: 0.7741 (ptpp) REVERT: D 528 TYR cc_start: 0.8447 (m-10) cc_final: 0.8062 (m-10) REVERT: D 634 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9111 (mmmm) REVERT: A 280 MET cc_start: 0.9384 (tmm) cc_final: 0.8516 (mmt) REVERT: B 528 TYR cc_start: 0.8770 (m-10) cc_final: 0.8506 (m-10) REVERT: B 556 MET cc_start: 0.8703 (tmm) cc_final: 0.8046 (tmm) REVERT: B 622 TRP cc_start: 0.9516 (OUTLIER) cc_final: 0.8273 (t60) REVERT: B 634 LYS cc_start: 0.9605 (mmtm) cc_final: 0.9111 (mmmm) REVERT: B 688 MET cc_start: 0.8491 (mtp) cc_final: 0.8231 (mtp) outliers start: 30 outliers final: 27 residues processed: 96 average time/residue: 0.1790 time to fit residues: 25.3579 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 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 591 CYS Chi-restraints excluded: chain B residue 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 476 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048445 restraints weight = 45239.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050181 restraints weight = 25884.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051386 restraints weight = 18245.926| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8955 Z= 0.131 Angle : 0.784 10.108 12321 Z= 0.366 Chirality : 0.047 0.297 1503 Planarity : 0.005 0.051 1494 Dihedral : 8.634 78.877 2100 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 3.37 % Allowed : 27.76 % Favored : 68.87 % 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: -1.11 (0.28), residues: 1054 helix: 0.92 (0.30), residues: 332 sheet: -1.25 (0.53), residues: 118 loop : -1.64 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 622 HIS 0.002 0.001 HIS A 336 PHE 0.035 0.002 PHE A 345 TYR 0.017 0.001 TYR B 709 ARG 0.001 0.000 ARG A 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 11) link_NAG-ASN : angle 3.48083 ( 33) link_BETA1-4 : bond 0.00675 ( 26) link_BETA1-4 : angle 1.95203 ( 78) hydrogen bonds : bond 0.03625 ( 283) hydrogen bonds : angle 5.10647 ( 795) SS BOND : bond 0.00199 ( 24) SS BOND : angle 1.02693 ( 48) covalent geometry : bond 0.00279 ( 8892) covalent geometry : angle 0.74929 (12162) Misc. bond : bond 0.00092 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2842.84 seconds wall clock time: 51 minutes 24.48 seconds (3084.48 seconds total)