Starting phenix.real_space_refine on Wed Sep 17 13:00:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rjj_19243/09_2025/8rjj_19243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rjj_19243/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rjj_19243/09_2025/8rjj_19243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rjj_19243/09_2025/8rjj_19243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rjj_19243/09_2025/8rjj_19243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rjj_19243/09_2025/8rjj_19243.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'HIS:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 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: {'TRP:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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, 'HIS:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 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: {'TRP:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: 2.61, per 1000 atoms: 0.30 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: 1.20 Conformation dependent library (CDL) restraints added in 385.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.38 Time building geometry restraints manager: 1.45 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: 0.01 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: 2.250 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- 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 : 18.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG D 620 TYR 0.019 0.002 TYR B 709 PHE 0.022 0.002 PHE A 285 TRP 0.026 0.001 TRP B 530 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8892) covalent geometry : angle 0.88194 (12162) SS BOND : bond 0.00324 ( 24) SS BOND : angle 1.02653 ( 48) hydrogen bonds : bond 0.14618 ( 283) hydrogen bonds : angle 6.33919 ( 795) Misc. bond : bond 0.00108 ( 2) link_BETA1-4 : bond 0.00579 ( 26) link_BETA1-4 : angle 2.35957 ( 78) link_NAG-ASN : bond 0.01270 ( 11) link_NAG-ASN : angle 3.94187 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.336 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: 0.0823 time to fit residues: 9.5853 Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.0020 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.1194 ------------------------------------------------------------------------------- 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 423 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047323 restraints weight = 47033.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049021 restraints weight = 26862.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050213 restraints weight = 18936.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050992 restraints weight = 15124.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051439 restraints weight = 13056.441| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1005 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= 0.208 Angle : 0.858 10.888 12321 Z= 0.398 Chirality : 0.050 0.340 1503 Planarity : 0.005 0.052 1494 Dihedral : 17.358 114.115 2100 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 5.05 % Allowed : 22.72 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.27), residues: 1054 helix: 0.82 (0.30), residues: 322 sheet: -2.16 (0.46), residues: 118 loop : -1.94 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 636 TYR 0.019 0.002 TYR D 709 PHE 0.022 0.002 PHE A 345 TRP 0.013 0.001 TRP B 530 HIS 0.004 0.001 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8892) covalent geometry : angle 0.81017 (12162) SS BOND : bond 0.00326 ( 24) SS BOND : angle 0.97319 ( 48) hydrogen bonds : bond 0.04503 ( 283) hydrogen bonds : angle 5.43750 ( 795) Misc. bond : bond 0.00068 ( 2) link_BETA1-4 : bond 0.00548 ( 26) link_BETA1-4 : angle 2.34289 ( 78) link_NAG-ASN : bond 0.01005 ( 11) link_NAG-ASN : angle 4.32842 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9674 (tp) cc_final: 0.9448 (pp) REVERT: C 280 MET cc_start: 0.9341 (tmm) cc_final: 0.8641 (mmt) REVERT: D 634 LYS cc_start: 0.9579 (mmtm) cc_final: 0.9133 (mmmt) REVERT: B 447 PHE cc_start: 0.8189 (t80) cc_final: 0.7975 (t80) REVERT: B 530 TRP cc_start: 0.8159 (m100) cc_final: 0.7884 (m100) REVERT: B 634 LYS cc_start: 0.9581 (mmtm) cc_final: 0.9082 (mmmm) outliers start: 42 outliers final: 19 residues processed: 112 average time/residue: 0.0713 time to fit residues: 12.4020 Evaluate side-chains 92 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 258 ILE 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 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 6 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS D 533 ASN D 706 GLN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.065641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048885 restraints weight = 46311.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050587 restraints weight = 26421.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051760 restraints weight = 18665.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052538 restraints weight = 14920.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052882 restraints weight = 12920.722| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8955 Z= 0.151 Angle : 0.829 11.119 12321 Z= 0.385 Chirality : 0.049 0.297 1503 Planarity : 0.005 0.052 1494 Dihedral : 14.536 114.715 2100 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 4.21 % Allowed : 23.80 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.27), residues: 1054 helix: 0.94 (0.30), residues: 322 sheet: -1.49 (0.52), residues: 92 loop : -1.99 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 665 TYR 0.020 0.002 TYR D 709 PHE 0.012 0.001 PHE A 345 TRP 0.013 0.001 TRP B 530 HIS 0.003 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8892) covalent geometry : angle 0.78115 (12162) SS BOND : bond 0.00315 ( 24) SS BOND : angle 1.39280 ( 48) hydrogen bonds : bond 0.04078 ( 283) hydrogen bonds : angle 5.23932 ( 795) Misc. bond : bond 0.00079 ( 2) link_BETA1-4 : bond 0.00677 ( 26) link_BETA1-4 : angle 2.06613 ( 78) link_NAG-ASN : bond 0.00957 ( 11) link_NAG-ASN : angle 4.34382 ( 33) *********************** 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 118 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9653 (tp) cc_final: 0.9414 (pp) REVERT: C 280 MET cc_start: 0.9344 (tmm) cc_final: 0.9108 (tmm) REVERT: D 634 LYS cc_start: 0.9578 (mmtm) cc_final: 0.9124 (mmmt) REVERT: B 447 PHE cc_start: 0.8078 (t80) cc_final: 0.7866 (t80) REVERT: B 528 TYR cc_start: 0.8727 (m-10) cc_final: 0.8397 (m-10) REVERT: B 634 LYS cc_start: 0.9584 (mmtm) cc_final: 0.9099 (mmmm) REVERT: B 688 MET cc_start: 0.8425 (mtp) cc_final: 0.8169 (mtp) outliers start: 35 outliers final: 16 residues processed: 111 average time/residue: 0.0755 time to fit residues: 12.7800 Evaluate side-chains 92 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.065018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048215 restraints weight = 47122.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049931 restraints weight = 26774.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.051069 restraints weight = 18934.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051772 restraints weight = 15167.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.052266 restraints weight = 13268.946| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1536 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= 0.173 Angle : 0.808 10.489 12321 Z= 0.377 Chirality : 0.048 0.305 1503 Planarity : 0.005 0.053 1494 Dihedral : 12.788 112.564 2100 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 3.85 % Allowed : 25.96 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.27), residues: 1054 helix: 1.07 (0.31), residues: 322 sheet: -1.19 (0.52), residues: 108 loop : -1.91 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 620 TYR 0.020 0.001 TYR D 709 PHE 0.011 0.001 PHE D 510 TRP 0.009 0.001 TRP D 652 HIS 0.004 0.001 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8892) covalent geometry : angle 0.76074 (12162) SS BOND : bond 0.00297 ( 24) SS BOND : angle 1.39641 ( 48) hydrogen bonds : bond 0.03913 ( 283) hydrogen bonds : angle 5.18766 ( 795) Misc. bond : bond 0.00096 ( 2) link_BETA1-4 : bond 0.00616 ( 26) link_BETA1-4 : angle 2.06924 ( 78) link_NAG-ASN : bond 0.00741 ( 11) link_NAG-ASN : angle 4.20914 ( 33) *********************** 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 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9666 (tp) cc_final: 0.9420 (pp) REVERT: C 280 MET cc_start: 0.9355 (tmm) cc_final: 0.9094 (tmm) REVERT: D 528 TYR cc_start: 0.8557 (m-10) cc_final: 0.8218 (m-10) REVERT: D 634 LYS cc_start: 0.9579 (mmtm) cc_final: 0.9144 (mmmt) REVERT: B 528 TYR cc_start: 0.8692 (m-10) cc_final: 0.8295 (m-10) REVERT: B 634 LYS cc_start: 0.9582 (mmtm) cc_final: 0.9096 (mmmm) REVERT: B 688 MET cc_start: 0.8448 (mtp) cc_final: 0.8187 (ttm) outliers start: 32 outliers final: 22 residues processed: 100 average time/residue: 0.0749 time to fit residues: 11.4506 Evaluate side-chains 93 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047383 restraints weight = 47141.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049062 restraints weight = 26914.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050193 restraints weight = 19085.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050970 restraints weight = 15348.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051395 restraints weight = 13329.004| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8955 Z= 0.221 Angle : 0.807 9.685 12321 Z= 0.381 Chirality : 0.048 0.288 1503 Planarity : 0.005 0.054 1494 Dihedral : 11.895 110.287 2100 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 5.41 % Allowed : 24.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.27), residues: 1054 helix: 1.28 (0.31), residues: 310 sheet: -1.67 (0.47), residues: 124 loop : -1.91 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.019 0.001 TYR D 709 PHE 0.009 0.001 PHE D 538 TRP 0.011 0.001 TRP B 420 HIS 0.005 0.001 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8892) covalent geometry : angle 0.76336 (12162) SS BOND : bond 0.00334 ( 24) SS BOND : angle 1.32562 ( 48) hydrogen bonds : bond 0.03966 ( 283) hydrogen bonds : angle 5.25329 ( 795) Misc. bond : bond 0.00059 ( 2) link_BETA1-4 : bond 0.00591 ( 26) link_BETA1-4 : angle 2.03761 ( 78) link_NAG-ASN : bond 0.00618 ( 11) link_NAG-ASN : angle 4.01991 ( 33) *********************** 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 115 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 70 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9661 (tp) cc_final: 0.9434 (pp) REVERT: D 634 LYS cc_start: 0.9580 (mmtm) cc_final: 0.9102 (mmmm) REVERT: A 280 MET cc_start: 0.9334 (tmm) cc_final: 0.8470 (mmt) REVERT: B 528 TYR cc_start: 0.8685 (m-10) cc_final: 0.8434 (m-10) REVERT: B 556 MET cc_start: 0.8666 (tmm) cc_final: 0.8448 (tmm) REVERT: B 634 LYS cc_start: 0.9592 (mmtm) cc_final: 0.9101 (mmmm) REVERT: B 688 MET cc_start: 0.8506 (mtp) cc_final: 0.8252 (mtp) outliers start: 45 outliers final: 28 residues processed: 107 average time/residue: 0.0715 time to fit residues: 11.7287 Evaluate side-chains 97 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR 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 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047071 restraints weight = 47683.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048734 restraints weight = 27416.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049879 restraints weight = 19524.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050635 restraints weight = 15664.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051041 restraints weight = 13608.095| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8955 Z= 0.249 Angle : 0.831 9.458 12321 Z= 0.394 Chirality : 0.048 0.278 1503 Planarity : 0.005 0.054 1494 Dihedral : 11.541 107.630 2100 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 4.45 % Allowed : 26.32 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.27), residues: 1054 helix: 1.11 (0.31), residues: 310 sheet: -1.72 (0.47), residues: 124 loop : -1.92 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 620 TYR 0.019 0.002 TYR D 709 PHE 0.018 0.001 PHE C 362 TRP 0.012 0.002 TRP B 420 HIS 0.006 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 8892) covalent geometry : angle 0.79051 (12162) SS BOND : bond 0.00365 ( 24) SS BOND : angle 1.26278 ( 48) hydrogen bonds : bond 0.04182 ( 283) hydrogen bonds : angle 5.39106 ( 795) Misc. bond : bond 0.00057 ( 2) link_BETA1-4 : bond 0.00565 ( 26) link_BETA1-4 : angle 2.04297 ( 78) link_NAG-ASN : bond 0.00568 ( 11) link_NAG-ASN : angle 3.88586 ( 33) *********************** 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 109 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9662 (tp) cc_final: 0.9428 (pp) REVERT: D 634 LYS cc_start: 0.9585 (mmtm) cc_final: 0.9106 (mmmm) REVERT: A 280 MET cc_start: 0.9340 (tmm) cc_final: 0.8454 (mmt) REVERT: B 528 TYR cc_start: 0.8682 (m-10) cc_final: 0.8452 (m-10) REVERT: B 556 MET cc_start: 0.8714 (tmm) cc_final: 0.8480 (tmm) REVERT: B 634 LYS cc_start: 0.9599 (mmtm) cc_final: 0.9116 (mmmm) outliers start: 37 outliers final: 31 residues processed: 101 average time/residue: 0.0802 time to fit residues: 12.0649 Evaluate side-chains 101 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 230 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 chunk 55 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047432 restraints weight = 47207.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.049113 restraints weight = 26919.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050264 restraints weight = 19046.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.051007 restraints weight = 15310.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051436 restraints weight = 13309.910| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8955 Z= 0.215 Angle : 0.807 9.681 12321 Z= 0.382 Chirality : 0.048 0.279 1503 Planarity : 0.005 0.055 1494 Dihedral : 10.996 103.218 2100 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 5.29 % Allowed : 26.08 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.27), residues: 1054 helix: 1.12 (0.31), residues: 310 sheet: -1.77 (0.47), residues: 124 loop : -1.90 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 593 TYR 0.019 0.001 TYR D 709 PHE 0.014 0.001 PHE C 362 TRP 0.019 0.002 TRP B 622 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8892) covalent geometry : angle 0.76935 (12162) SS BOND : bond 0.00315 ( 24) SS BOND : angle 1.19990 ( 48) hydrogen bonds : bond 0.04118 ( 283) hydrogen bonds : angle 5.32366 ( 795) Misc. bond : bond 0.00067 ( 2) link_BETA1-4 : bond 0.00590 ( 26) link_BETA1-4 : angle 1.97243 ( 78) link_NAG-ASN : bond 0.00569 ( 11) link_NAG-ASN : angle 3.68909 ( 33) *********************** 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 116 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.9667 (tp) cc_final: 0.9431 (pp) REVERT: D 405 MET cc_start: 0.8657 (tpp) cc_final: 0.8027 (ppp) REVERT: D 634 LYS cc_start: 0.9581 (mmtm) cc_final: 0.9099 (mmmm) REVERT: A 280 MET cc_start: 0.9340 (tmm) cc_final: 0.8459 (mmt) REVERT: B 528 TYR cc_start: 0.8725 (m-10) cc_final: 0.8471 (m-10) REVERT: B 556 MET cc_start: 0.8756 (tmm) cc_final: 0.8481 (tmm) REVERT: B 634 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9115 (mmmm) REVERT: B 688 MET cc_start: 0.8514 (mtp) cc_final: 0.8116 (mtp) outliers start: 44 outliers final: 34 residues processed: 105 average time/residue: 0.0734 time to fit residues: 11.8772 Evaluate side-chains 105 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 265 LEU 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 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 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 255 THR 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 427 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 678 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.065418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048486 restraints weight = 45192.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050216 restraints weight = 25856.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051429 restraints weight = 18236.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052204 restraints weight = 14525.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052714 restraints weight = 12566.866| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2209 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= 0.140 Angle : 0.784 10.154 12321 Z= 0.370 Chirality : 0.047 0.282 1503 Planarity : 0.005 0.054 1494 Dihedral : 10.206 97.960 2100 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 3.85 % Allowed : 27.76 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.27), residues: 1054 helix: 0.91 (0.30), residues: 332 sheet: -1.42 (0.51), residues: 118 loop : -1.75 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 612 TYR 0.020 0.001 TYR B 709 PHE 0.009 0.001 PHE C 362 TRP 0.014 0.001 TRP B 622 HIS 0.004 0.001 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8892) covalent geometry : angle 0.74865 (12162) SS BOND : bond 0.00213 ( 24) SS BOND : angle 1.06721 ( 48) hydrogen bonds : bond 0.03808 ( 283) hydrogen bonds : angle 5.15752 ( 795) Misc. bond : bond 0.00091 ( 2) link_BETA1-4 : bond 0.00698 ( 26) link_BETA1-4 : angle 1.87696 ( 78) link_NAG-ASN : bond 0.00711 ( 11) link_NAG-ASN : angle 3.58944 ( 33) *********************** 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 109 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 405 MET cc_start: 0.8564 (tpp) cc_final: 0.7874 (ppp) REVERT: D 528 TYR cc_start: 0.8575 (m-10) cc_final: 0.8156 (m-10) REVERT: D 634 LYS cc_start: 0.9590 (mmtm) cc_final: 0.9052 (mmmm) REVERT: B 528 TYR cc_start: 0.8695 (m-10) cc_final: 0.8414 (m-10) REVERT: B 556 MET cc_start: 0.8774 (tmm) cc_final: 0.8483 (tmm) REVERT: B 634 LYS cc_start: 0.9598 (mmtm) cc_final: 0.9104 (mmmm) REVERT: B 688 MET cc_start: 0.8493 (mtp) cc_final: 0.8129 (mtp) outliers start: 32 outliers final: 30 residues processed: 104 average time/residue: 0.0823 time to fit residues: 12.6889 Evaluate side-chains 101 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 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 231 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** 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 = 0.3429 r_free = 0.3429 target = 0.064417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047608 restraints weight = 46806.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049286 restraints weight = 26771.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050395 restraints weight = 18957.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051186 restraints weight = 15264.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051553 restraints weight = 13232.573| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2269 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 10.880 12321 Z= 0.376 Chirality : 0.047 0.286 1503 Planarity : 0.005 0.051 1494 Dihedral : 9.801 91.498 2100 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 3.61 % Allowed : 28.97 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.27), residues: 1054 helix: 0.99 (0.31), residues: 322 sheet: -1.14 (0.57), residues: 96 loop : -1.82 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 593 TYR 0.019 0.001 TYR B 709 PHE 0.013 0.001 PHE C 362 TRP 0.012 0.002 TRP B 622 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8892) covalent geometry : angle 0.76096 (12162) SS BOND : bond 0.00290 ( 24) SS BOND : angle 1.13658 ( 48) hydrogen bonds : bond 0.03977 ( 283) hydrogen bonds : angle 5.25596 ( 795) Misc. bond : bond 0.00065 ( 2) link_BETA1-4 : bond 0.00598 ( 26) link_BETA1-4 : angle 2.06197 ( 78) link_NAG-ASN : bond 0.00564 ( 11) link_NAG-ASN : angle 3.52487 ( 33) *********************** 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 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 528 TYR cc_start: 0.8512 (m-10) cc_final: 0.8115 (m-10) REVERT: D 634 LYS cc_start: 0.9550 (mmtm) cc_final: 0.9091 (mmmm) REVERT: D 668 GLN cc_start: 0.9079 (mt0) cc_final: 0.8869 (mt0) REVERT: A 280 MET cc_start: 0.9338 (tmm) cc_final: 0.8490 (mmt) REVERT: B 528 TYR cc_start: 0.8738 (m-10) cc_final: 0.8446 (m-10) REVERT: B 556 MET cc_start: 0.8789 (tmm) cc_final: 0.8047 (tmm) REVERT: B 622 TRP cc_start: 0.9514 (OUTLIER) cc_final: 0.8255 (t60) REVERT: B 634 LYS cc_start: 0.9608 (mmtm) cc_final: 0.9112 (mmmm) REVERT: B 688 MET cc_start: 0.8546 (mtp) cc_final: 0.8172 (mtp) outliers start: 30 outliers final: 27 residues processed: 95 average time/residue: 0.0768 time to fit residues: 11.0836 Evaluate side-chains 97 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 303 THR 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 255 THR Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.065504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048656 restraints weight = 46445.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050333 restraints weight = 26642.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051494 restraints weight = 18756.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.052305 restraints weight = 15018.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052812 restraints weight = 12976.613| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8955 Z= 0.143 Angle : 0.794 10.559 12321 Z= 0.374 Chirality : 0.047 0.290 1503 Planarity : 0.005 0.050 1494 Dihedral : 9.310 86.492 2100 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 3.73 % Allowed : 28.97 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.27), residues: 1054 helix: 0.83 (0.30), residues: 334 sheet: -1.41 (0.52), residues: 118 loop : -1.77 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 665 TYR 0.020 0.001 TYR B 709 PHE 0.028 0.001 PHE A 285 TRP 0.014 0.001 TRP B 622 HIS 0.002 0.001 HIS D 595 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8892) covalent geometry : angle 0.76036 (12162) SS BOND : bond 0.00217 ( 24) SS BOND : angle 1.03822 ( 48) hydrogen bonds : bond 0.03820 ( 283) hydrogen bonds : angle 5.20184 ( 795) Misc. bond : bond 0.00084 ( 2) link_BETA1-4 : bond 0.00640 ( 26) link_BETA1-4 : angle 1.94985 ( 78) link_NAG-ASN : bond 0.00674 ( 11) link_NAG-ASN : angle 3.45926 ( 33) ********************** 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 106 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 528 TYR cc_start: 0.8485 (m-10) cc_final: 0.8099 (m-10) REVERT: D 634 LYS cc_start: 0.9553 (mmtm) cc_final: 0.9077 (mmmm) REVERT: D 668 GLN cc_start: 0.9096 (mt0) cc_final: 0.8839 (mt0) REVERT: A 280 MET cc_start: 0.9340 (tmm) cc_final: 0.8495 (mmt) REVERT: B 528 TYR cc_start: 0.8695 (m-10) cc_final: 0.8371 (m-10) REVERT: B 556 MET cc_start: 0.8761 (tmm) cc_final: 0.7971 (tmm) REVERT: B 622 TRP cc_start: 0.9499 (OUTLIER) cc_final: 0.8188 (t60) REVERT: B 634 LYS cc_start: 0.9607 (mmtm) cc_final: 0.9110 (mmmm) REVERT: B 688 MET cc_start: 0.8509 (mtp) cc_final: 0.8149 (mtp) outliers start: 31 outliers final: 26 residues processed: 102 average time/residue: 0.0821 time to fit residues: 12.3031 Evaluate side-chains 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 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 255 THR Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 622 TRP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** 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 = 0.3444 r_free = 0.3444 target = 0.064954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048106 restraints weight = 46233.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049788 restraints weight = 26481.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050908 restraints weight = 18791.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.051720 restraints weight = 15122.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052053 restraints weight = 13098.910| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2463 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= 0.175 Angle : 0.813 13.176 12321 Z= 0.381 Chirality : 0.047 0.288 1503 Planarity : 0.005 0.052 1494 Dihedral : 8.922 79.346 2100 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.37 % Allowed : 29.33 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.27), residues: 1054 helix: 0.93 (0.31), residues: 322 sheet: -1.08 (0.57), residues: 96 loop : -1.81 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 593 TYR 0.018 0.001 TYR D 709 PHE 0.011 0.001 PHE C 362 TRP 0.012 0.001 TRP B 622 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8892) covalent geometry : angle 0.77782 (12162) SS BOND : bond 0.00262 ( 24) SS BOND : angle 1.09336 ( 48) hydrogen bonds : bond 0.03902 ( 283) hydrogen bonds : angle 5.19034 ( 795) Misc. bond : bond 0.00069 ( 2) link_BETA1-4 : bond 0.00580 ( 26) link_BETA1-4 : angle 2.07435 ( 78) link_NAG-ASN : bond 0.00589 ( 11) link_NAG-ASN : angle 3.42233 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1566.68 seconds wall clock time: 28 minutes 6.58 seconds (1686.58 seconds total)