Starting phenix.real_space_refine on Thu Aug 6 00:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9you_73278/08_2026/9you_73278.cif Found real_map, /net/cci-nas-00/data/ceres_data/9you_73278/08_2026/9you_73278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9you_73278/08_2026/9you_73278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9you_73278/08_2026/9you_73278.map" model { file = "/net/cci-nas-00/data/ceres_data/9you_73278/08_2026/9you_73278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9you_73278/08_2026/9you_73278.cif" } resolution = 4.0 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= -0.000 sd= 0.015 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 156 5.16 5 C 7376 2.51 5 N 2094 2.21 5 O 2418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12044 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5835 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 25, 'TRANS': 714} Chain: "B" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5835 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 25, 'TRANS': 714} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: "A" 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: 2.55, per 1000 atoms: 0.21 Number of scatterers: 12044 At special positions: 0 Unit cell: (110.137, 155.925, 163.35, 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 156 16.00 O 2418 8.00 N 2094 7.00 C 7376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 66 " distance=2.03 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 251 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 262 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 368 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 588 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 625 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 637 " distance=2.03 Simple disulfide: pdb=" SG CYS A 640 " - pdb=" SG CYS A 653 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS A 693 " - pdb=" SG CYS A 708 " distance=2.03 Simple disulfide: pdb=" SG CYS A 710 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 746 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 66 " distance=2.03 Simple disulfide: pdb=" SG CYS B 181 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 251 " distance=2.03 Simple disulfide: pdb=" SG CYS B 248 " - pdb=" SG CYS B 262 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 267 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 364 " distance=2.03 Simple disulfide: pdb=" SG CYS B 368 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 513 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 574 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 625 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 637 " distance=2.03 Simple disulfide: pdb=" SG CYS B 640 " - pdb=" SG CYS B 653 " distance=2.03 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 686 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 696 " distance=2.03 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS B 708 " distance=2.03 Simple disulfide: pdb=" SG CYS B 710 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 764 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 901 " - " ASN A 91 " " NAG B 901 " - " ASN B 91 " " NAG C 1 " - " ASN A 169 " " NAG D 1 " - " ASN A 255 " " NAG E 1 " - " ASN A 376 " " NAG F 1 " - " ASN A 561 " " NAG G 1 " - " ASN A 648 " " NAG H 1 " - " ASN B 169 " " NAG I 1 " - " ASN B 255 " " NAG J 1 " - " ASN B 376 " " NAG K 1 " - " ASN B 561 " " NAG L 1 " - " ASN B 648 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 481.7 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 35 sheets defined 14.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.708A pdb=" N ASP A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.548A pdb=" N LEU A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.580A pdb=" N CYS A 236 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 382 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.785A pdb=" N VAL A 405 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 481 through 485 removed outlier: 4.108A pdb=" N ILE A 485 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 4.092A pdb=" N ILE A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.792A pdb=" N CYS A 537 " --> pdb=" O PRO A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 760 through 764 removed outlier: 4.045A pdb=" N CYS A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.628A pdb=" N ASP B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.710A pdb=" N ARG B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.500A pdb=" N GLU B 99 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.854A pdb=" N LEU B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.613A pdb=" N CYS B 236 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 375 through 382 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.089A pdb=" N THR B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.589A pdb=" N ILE B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.623A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.749A pdb=" N CYS B 537 " --> pdb=" O PRO B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 760 through 764 removed outlier: 4.055A pdb=" N CYS B 764 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 5.825A pdb=" N CYS A 32 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 39 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N CYS A 38 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 69 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 114 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 69 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 78 removed outlier: 7.371A pdb=" N GLU A 74 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 121 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A 76 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A 123 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 119 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR A 149 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS A 151 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG A 123 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN A 146 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 173 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 148 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN A 175 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 150 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 172 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.935A pdb=" N ILE A 137 " --> pdb=" O VAL A 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 254 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.587A pdb=" N ALA A 281 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY A 270 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 279 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA8, first strand: chain 'A' and resid 299 through 302 removed outlier: 3.516A pdb=" N ARG A 307 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 318 Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 333 Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AB3, first strand: chain 'A' and resid 367 through 368 removed outlier: 4.141A pdb=" N VAL A 412 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 392 through 394 removed outlier: 5.761A pdb=" N LEU A 392 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 419 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE A 394 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 416 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N TYR A 450 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 418 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP A 445 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 472 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A 447 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET A 474 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE A 449 " --> pdb=" O MET A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 548 through 550 removed outlier: 6.424A pdb=" N LYS A 544 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG A 569 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 566 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 561 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 568 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 605 through 607 Processing sheet with id=AB7, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.409A pdb=" N ALA A 643 " --> pdb=" O CYS A 686 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LYS A 688 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 685 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 674 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 713 through 715 Processing sheet with id=AB9, first strand: chain 'A' and resid 732 through 733 removed outlier: 3.636A pdb=" N PHE A 733 " --> pdb=" O LYS A 744 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 744 " --> pdb=" O PHE A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.664A pdb=" N SER B 34 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.732A pdb=" N VAL B 69 " --> pdb=" O GLU B 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 73 through 78 removed outlier: 7.017A pdb=" N GLU B 74 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 121 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B 76 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG B 123 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 149 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS B 151 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG B 123 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B 146 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B 173 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 148 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN B 175 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 150 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL B 172 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 136 through 137 removed outlier: 3.826A pdb=" N ILE B 137 " --> pdb=" O VAL B 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 211 through 212 Processing sheet with id=AC6, first strand: chain 'B' and resid 251 through 254 Processing sheet with id=AC7, first strand: chain 'B' and resid 267 through 271 removed outlier: 7.615A pdb=" N GLY B 270 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N CYS B 279 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AC9, first strand: chain 'B' and resid 299 through 302 removed outlier: 3.622A pdb=" N ARG B 307 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 316 through 318 Processing sheet with id=AD2, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AD3, first strand: chain 'B' and resid 367 through 368 removed outlier: 3.838A pdb=" N VAL B 412 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 392 through 394 removed outlier: 3.512A pdb=" N VAL B 419 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 416 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N TYR B 450 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 418 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP B 445 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 472 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU B 447 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET B 474 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE B 449 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN B 476 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA B 505 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 473 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN B 507 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS B 475 " --> pdb=" O ASN B 507 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 548 through 550 removed outlier: 6.278A pdb=" N LYS B 544 " --> pdb=" O CYS B 567 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG B 569 " --> pdb=" O LYS B 544 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 568 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 606 through 607 Processing sheet with id=AD7, first strand: chain 'B' and resid 651 through 654 removed outlier: 3.657A pdb=" N PHE B 652 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 642 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS B 688 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS B 685 " --> pdb=" O SER B 674 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 674 " --> pdb=" O HIS B 685 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.617A pdb=" N VAL B 713 " --> pdb=" O MET B 725 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 725 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 715 " --> pdb=" O ILE B 723 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.27 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: 3983 1.34 - 1.46: 2326 1.46 - 1.58: 5783 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 12266 Sorted by residual: bond pdb=" CB ARG B 123 " pdb=" CG ARG B 123 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.61e+00 bond pdb=" N ASN B 91 " pdb=" CA ASN B 91 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CB MET A 565 " pdb=" CG MET A 565 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" N GLU B 506 " pdb=" CA GLU B 506 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.33e+00 bond pdb=" N VAL B 243 " pdb=" CA VAL B 243 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.13e+00 ... (remaining 12261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 16382 2.63 - 5.27: 158 5.27 - 7.90: 16 7.90 - 10.54: 2 10.54 - 13.17: 2 Bond angle restraints: 16560 Sorted by residual: angle pdb=" C ASN A 225 " pdb=" CA ASN A 225 " pdb=" CB ASN A 225 " ideal model delta sigma weight residual 117.23 110.47 6.76 1.36e+00 5.41e-01 2.47e+01 angle pdb=" C ASN B 225 " pdb=" CA ASN B 225 " pdb=" CB ASN B 225 " ideal model delta sigma weight residual 117.23 110.62 6.61 1.36e+00 5.41e-01 2.37e+01 angle pdb=" CB MET A 565 " pdb=" CG MET A 565 " pdb=" SD MET A 565 " ideal model delta sigma weight residual 112.70 125.87 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CA MET A 565 " pdb=" CB MET A 565 " pdb=" CG MET A 565 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA ASN A 225 " pdb=" C ASN A 225 " pdb=" N ASP A 226 " ideal model delta sigma weight residual 119.98 116.82 3.16 8.50e-01 1.38e+00 1.38e+01 ... (remaining 16555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 7422 25.70 - 51.39: 393 51.39 - 77.09: 117 77.09 - 102.79: 66 102.79 - 128.48: 50 Dihedral angle restraints: 8048 sinusoidal: 3736 harmonic: 4312 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 228 " pdb=" CB CYS A 228 " ideal model delta sinusoidal sigma weight residual -86.00 -169.77 83.77 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 359 " pdb=" SG CYS A 359 " pdb=" SG CYS A 364 " pdb=" CB CYS A 364 " ideal model delta sinusoidal sigma weight residual 93.00 16.09 76.91 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS B 228 " pdb=" CB CYS B 228 " ideal model delta sinusoidal sigma weight residual -86.00 -162.59 76.59 1 1.00e+01 1.00e-02 7.37e+01 ... (remaining 8045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1581 0.062 - 0.125: 260 0.125 - 0.187: 33 0.187 - 0.249: 4 0.249 - 0.312: 2 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CB ILE A 473 " pdb=" CA ILE A 473 " pdb=" CG1 ILE A 473 " pdb=" CG2 ILE A 473 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE B 473 " pdb=" CA ILE B 473 " pdb=" CG1 ILE B 473 " pdb=" CG2 ILE B 473 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1877 not shown) Planarity restraints: 2138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 152 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C LYS B 152 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS B 152 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 153 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 145 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" CG ASP A 145 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 145 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 145 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 145 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ASP A 145 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP A 145 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 146 " 0.013 2.00e-02 2.50e+03 ... (remaining 2135 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 478 2.71 - 3.25: 12339 3.25 - 3.80: 19596 3.80 - 4.35: 24991 4.35 - 4.90: 39861 Nonbonded interactions: 97265 Sorted by model distance: nonbonded pdb=" OD2 ASP A 348 " pdb=" OG1 THR A 350 " model vdw 2.157 3.040 nonbonded pdb=" OD2 ASP B 348 " pdb=" OG1 THR B 350 " model vdw 2.171 3.040 nonbonded pdb=" OG SER A 254 " pdb=" OG1 THR A 257 " model vdw 2.196 3.040 nonbonded pdb=" O ASP B 188 " pdb=" NE2 GLN B 237 " model vdw 2.233 3.120 nonbonded pdb=" OG SER B 254 " pdb=" OG1 THR B 257 " model vdw 2.238 3.040 ... (remaining 97260 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 'B' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.470 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.003 0.057 12362 Z= 0.140 Angle : 0.697 13.171 16780 Z= 0.391 Chirality : 0.048 0.312 1880 Planarity : 0.004 0.086 2126 Dihedral : 21.327 128.485 5068 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.57 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1476 helix: -1.21 (0.47), residues: 116 sheet: -1.43 (0.49), residues: 121 loop : -0.69 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 123 TYR 0.029 0.001 TYR B 122 PHE 0.009 0.001 PHE A 428 TRP 0.017 0.001 TRP B 86 HIS 0.009 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (12266) covalent geometry : angle 0.68657 / 0.39 (16560) SS BOND : bond 0.00164 / 0.10 ( 68) SS BOND : angle 0.67496 / 0.52 ( 136) hydrogen bonds : bond 0.26367 / 17.09 ( 165) hydrogen bonds : angle 10.11618 / 6.72 ( 342) link_ALPHA1-3 : bond 0.00738 / 0.37 ( 2) link_ALPHA1-3 : angle 1.46893 / 0.86 ( 6) link_BETA1-4 : bond 0.00669 / 0.42 ( 14) link_BETA1-4 : angle 1.23337 / 0.83 ( 42) link_NAG-ASN : bond 0.00353 / 0.16 ( 12) link_NAG-ASN : angle 2.36192 / 1.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.9011 (mmp) cc_final: 0.8588 (mmm) REVERT: B 205 ASN cc_start: 0.9499 (p0) cc_final: 0.9234 (t0) REVERT: B 659 MET cc_start: 0.3084 (tpt) cc_final: 0.2850 (tpt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0819 time to fit residues: 8.9590 Evaluate side-chains 51 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 HIS A 623 ASN A 639 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.081892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.050565 restraints weight = 140637.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.048636 restraints weight = 117580.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.049008 restraints weight = 92800.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.049524 restraints weight = 78997.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.049409 restraints weight = 71764.625| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12362 Z= 0.150 Angle : 0.704 9.070 16780 Z= 0.334 Chirality : 0.051 0.261 1880 Planarity : 0.004 0.040 2126 Dihedral : 21.104 115.450 2176 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.38 % Favored : 92.34 % Rotamer: Outliers : 0.44 % Allowed : 5.01 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1476 helix: -1.41 (0.45), residues: 119 sheet: -0.65 (0.52), residues: 123 loop : -0.60 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 123 TYR 0.016 0.002 TYR A 450 PHE 0.008 0.002 PHE A 301 TRP 0.007 0.001 TRP B 530 HIS 0.005 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (12266) covalent geometry : angle 0.67702 / 0.33 (16560) SS BOND : bond 0.00335 / 0.22 ( 68) SS BOND : angle 0.85381 / 0.63 ( 136) hydrogen bonds : bond 0.03424 / 2.33 ( 165) hydrogen bonds : angle 7.78591 / 5.16 ( 342) link_ALPHA1-3 : bond 0.01393 / 0.69 ( 2) link_ALPHA1-3 : angle 2.04425 / 1.34 ( 6) link_BETA1-4 : bond 0.00554 / 0.32 ( 14) link_BETA1-4 : angle 2.82348 / 1.95 ( 42) link_NAG-ASN : bond 0.00403 / 0.22 ( 12) link_NAG-ASN : angle 2.78074 / 1.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.9236 (pmm) cc_final: 0.8971 (pmm) REVERT: A 474 MET cc_start: 0.9096 (mmp) cc_final: 0.8614 (mmm) REVERT: B 474 MET cc_start: 0.9199 (mmm) cc_final: 0.8989 (mmm) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.0971 time to fit residues: 9.3383 Evaluate side-chains 49 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 451 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 7.9990 chunk 124 optimal weight: 0.0270 chunk 104 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 340 HIS A 476 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 476 ASN B 507 ASN B 590 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.079932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.048920 restraints weight = 141720.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.047717 restraints weight = 116164.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.047446 restraints weight = 100046.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.047409 restraints weight = 86992.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.047454 restraints weight = 79656.113| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12362 Z= 0.152 Angle : 0.682 9.706 16780 Z= 0.322 Chirality : 0.048 0.228 1880 Planarity : 0.004 0.042 2126 Dihedral : 17.939 115.466 2176 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.25 % Favored : 92.48 % Rotamer: Outliers : 0.81 % Allowed : 7.60 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.22), residues: 1476 helix: -1.38 (0.45), residues: 124 sheet: -0.69 (0.49), residues: 138 loop : -0.61 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.023 0.002 TYR B 63 PHE 0.010 0.002 PHE A 301 TRP 0.010 0.001 TRP B 530 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (12266) covalent geometry : angle 0.65515 / 0.32 (16560) SS BOND : bond 0.00302 / 0.20 ( 68) SS BOND : angle 0.80459 / 0.58 ( 136) hydrogen bonds : bond 0.03470 / 2.35 ( 165) hydrogen bonds : angle 7.33986 / 4.86 ( 342) link_ALPHA1-3 : bond 0.01606 / 0.77 ( 2) link_ALPHA1-3 : angle 2.78109 / 1.69 ( 6) link_BETA1-4 : bond 0.00528 / 0.30 ( 14) link_BETA1-4 : angle 2.80359 / 1.99 ( 42) link_NAG-ASN : bond 0.00394 / 0.21 ( 12) link_NAG-ASN : angle 2.48849 / 1.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.9205 (pmm) cc_final: 0.8990 (pmm) REVERT: A 474 MET cc_start: 0.9039 (mmp) cc_final: 0.8559 (mmm) REVERT: B 474 MET cc_start: 0.9244 (mmm) cc_final: 0.8772 (mmm) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.0903 time to fit residues: 9.1151 Evaluate side-chains 52 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.078775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.043976 restraints weight = 141580.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.044007 restraints weight = 111845.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.043978 restraints weight = 98897.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.044002 restraints weight = 90550.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.044996 restraints weight = 87152.472| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12362 Z= 0.160 Angle : 0.701 10.113 16780 Z= 0.327 Chirality : 0.048 0.258 1880 Planarity : 0.004 0.038 2126 Dihedral : 15.857 111.849 2176 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.45 % Favored : 92.28 % Rotamer: Outliers : 1.03 % Allowed : 8.55 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.22), residues: 1476 helix: -1.37 (0.46), residues: 124 sheet: -0.87 (0.47), residues: 148 loop : -0.58 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 560 TYR 0.012 0.001 TYR A 138 PHE 0.009 0.002 PHE A 301 TRP 0.009 0.001 TRP B 530 HIS 0.005 0.001 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12266) covalent geometry : angle 0.67142 / 0.32 (16560) SS BOND : bond 0.00374 / 0.23 ( 68) SS BOND : angle 0.85881 / 0.62 ( 136) hydrogen bonds : bond 0.02893 / 1.99 ( 165) hydrogen bonds : angle 7.11345 / 4.68 ( 342) link_ALPHA1-3 : bond 0.02092 / 1.02 ( 2) link_ALPHA1-3 : angle 2.54054 / 1.48 ( 6) link_BETA1-4 : bond 0.00510 / 0.31 ( 14) link_BETA1-4 : angle 3.15109 / 2.22 ( 42) link_NAG-ASN : bond 0.00385 / 0.21 ( 12) link_NAG-ASN : angle 2.54876 / 1.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.9083 (mmp) cc_final: 0.8630 (mmm) REVERT: B 474 MET cc_start: 0.9327 (mmm) cc_final: 0.8872 (mmm) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.0936 time to fit residues: 8.5060 Evaluate side-chains 51 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 451 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS B 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.078728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.047229 restraints weight = 143358.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.047571 restraints weight = 122660.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.047308 restraints weight = 108997.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.047386 restraints weight = 105862.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.046998 restraints weight = 104122.011| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12362 Z= 0.129 Angle : 0.685 11.670 16780 Z= 0.316 Chirality : 0.048 0.244 1880 Planarity : 0.003 0.033 2126 Dihedral : 14.307 111.096 2176 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.45 % Favored : 92.28 % Rotamer: Outliers : 1.40 % Allowed : 8.92 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1476 helix: -1.45 (0.45), residues: 125 sheet: -0.73 (0.49), residues: 137 loop : -0.52 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 589 TYR 0.014 0.001 TYR B 260 PHE 0.007 0.001 PHE B 606 TRP 0.007 0.001 TRP B 445 HIS 0.004 0.001 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (12266) covalent geometry : angle 0.65374 / 0.31 (16560) SS BOND : bond 0.00264 / 0.17 ( 68) SS BOND : angle 0.89099 / 0.61 ( 136) hydrogen bonds : bond 0.02689 / 1.86 ( 165) hydrogen bonds : angle 6.87692 / 4.53 ( 342) link_ALPHA1-3 : bond 0.02178 / 1.05 ( 2) link_ALPHA1-3 : angle 2.87546 / 1.68 ( 6) link_BETA1-4 : bond 0.00558 / 0.35 ( 14) link_BETA1-4 : angle 3.13610 / 2.24 ( 42) link_NAG-ASN : bond 0.00295 / 0.15 ( 12) link_NAG-ASN : angle 2.52722 / 1.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.9100 (mmp) cc_final: 0.8601 (mmm) REVERT: B 474 MET cc_start: 0.9276 (mmm) cc_final: 0.8845 (mmm) outliers start: 19 outliers final: 9 residues processed: 59 average time/residue: 0.1008 time to fit residues: 9.4555 Evaluate side-chains 52 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.074312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.042543 restraints weight = 146584.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.042456 restraints weight = 124889.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.042662 restraints weight = 111080.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.042181 restraints weight = 110298.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.042440 restraints weight = 102096.793| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12362 Z= 0.289 Angle : 0.836 10.366 16780 Z= 0.409 Chirality : 0.050 0.268 1880 Planarity : 0.005 0.046 2126 Dihedral : 13.602 115.584 2176 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.08 % Favored : 90.65 % Rotamer: Outliers : 1.33 % Allowed : 10.77 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1476 helix: -1.43 (0.45), residues: 124 sheet: -0.91 (0.48), residues: 143 loop : -0.70 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 135 TYR 0.021 0.002 TYR A 138 PHE 0.015 0.003 PHE B 423 TRP 0.017 0.003 TRP B 530 HIS 0.011 0.002 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.29 (12266) covalent geometry : angle 0.80220 / 0.40 (16560) SS BOND : bond 0.00594 / 0.38 ( 68) SS BOND : angle 1.62556 / 1.15 ( 136) hydrogen bonds : bond 0.03805 / 2.65 ( 165) hydrogen bonds : angle 7.35148 / 4.80 ( 342) link_ALPHA1-3 : bond 0.01824 / 0.88 ( 2) link_ALPHA1-3 : angle 2.45742 / 1.43 ( 6) link_BETA1-4 : bond 0.00524 / 0.33 ( 14) link_BETA1-4 : angle 3.25220 / 2.25 ( 42) link_NAG-ASN : bond 0.00680 / 0.43 ( 12) link_NAG-ASN : angle 2.57644 / 1.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7326 (mm) REVERT: A 474 MET cc_start: 0.9215 (mmp) cc_final: 0.8820 (mmm) REVERT: B 473 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9149 (pt) REVERT: B 474 MET cc_start: 0.9294 (mmm) cc_final: 0.8892 (mmm) REVERT: B 620 CYS cc_start: -0.0274 (OUTLIER) cc_final: -0.0595 (m) outliers start: 18 outliers final: 13 residues processed: 56 average time/residue: 0.1033 time to fit residues: 9.3336 Evaluate side-chains 54 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 143 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** B 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.073691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.044556 restraints weight = 146401.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.044389 restraints weight = 131677.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.044124 restraints weight = 119488.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.044008 restraints weight = 111551.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.043166 restraints weight = 94949.803| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12362 Z= 0.232 Angle : 0.779 12.563 16780 Z= 0.379 Chirality : 0.048 0.237 1880 Planarity : 0.004 0.048 2126 Dihedral : 12.920 121.829 2176 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.81 % Favored : 90.92 % Rotamer: Outliers : 1.11 % Allowed : 12.61 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1476 helix: -1.43 (0.45), residues: 125 sheet: -1.25 (0.45), residues: 155 loop : -0.77 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 560 TYR 0.022 0.002 TYR A 138 PHE 0.016 0.002 PHE A 558 TRP 0.015 0.002 TRP A 86 HIS 0.007 0.002 HIS B 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (12266) covalent geometry : angle 0.74599 / 0.37 (16560) SS BOND : bond 0.00423 / 0.27 ( 68) SS BOND : angle 1.22539 / 0.84 ( 136) hydrogen bonds : bond 0.03281 / 2.28 ( 165) hydrogen bonds : angle 7.43441 / 4.86 ( 342) link_ALPHA1-3 : bond 0.02056 / 0.98 ( 2) link_ALPHA1-3 : angle 2.86238 / 1.67 ( 6) link_BETA1-4 : bond 0.00452 / 0.27 ( 14) link_BETA1-4 : angle 3.17811 / 2.30 ( 42) link_NAG-ASN : bond 0.00524 / 0.33 ( 12) link_NAG-ASN : angle 2.86598 / 1.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 474 MET cc_start: 0.9221 (mmp) cc_final: 0.8759 (mmp) REVERT: B 213 ASN cc_start: 0.9368 (m110) cc_final: 0.8864 (p0) REVERT: B 474 MET cc_start: 0.9378 (mmm) cc_final: 0.8881 (mmm) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.0949 time to fit residues: 8.2417 Evaluate side-chains 51 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 451 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 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 = 0.3891 r_free = 0.3891 target = 0.074583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.043751 restraints weight = 144487.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.043416 restraints weight = 121892.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.043368 restraints weight = 108024.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.043368 restraints weight = 107275.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.043177 restraints weight = 106315.860| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12362 Z= 0.159 Angle : 0.709 9.619 16780 Z= 0.338 Chirality : 0.048 0.250 1880 Planarity : 0.004 0.041 2126 Dihedral : 12.307 118.573 2176 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.33 % Favored : 91.40 % Rotamer: Outliers : 1.11 % Allowed : 12.98 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.22), residues: 1476 helix: -1.24 (0.47), residues: 124 sheet: -1.04 (0.51), residues: 125 loop : -0.72 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 238 TYR 0.016 0.002 TYR A 260 PHE 0.009 0.002 PHE B 423 TRP 0.014 0.002 TRP A 543 HIS 0.005 0.001 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (12266) covalent geometry : angle 0.67586 / 0.33 (16560) SS BOND : bond 0.00379 / 0.25 ( 68) SS BOND : angle 1.03929 / 0.72 ( 136) hydrogen bonds : bond 0.02863 / 1.96 ( 165) hydrogen bonds : angle 7.20781 / 4.71 ( 342) link_ALPHA1-3 : bond 0.02199 / 1.05 ( 2) link_ALPHA1-3 : angle 2.84252 / 1.68 ( 6) link_BETA1-4 : bond 0.00403 / 0.24 ( 14) link_BETA1-4 : angle 3.20862 / 2.36 ( 42) link_NAG-ASN : bond 0.00394 / 0.24 ( 12) link_NAG-ASN : angle 2.60011 / 1.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7400 (mm) REVERT: A 474 MET cc_start: 0.9165 (mmp) cc_final: 0.8728 (mmm) REVERT: B 213 ASN cc_start: 0.9559 (m110) cc_final: 0.9113 (p0) REVERT: B 473 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9214 (pt) REVERT: B 474 MET cc_start: 0.9309 (mmm) cc_final: 0.8774 (mmm) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.0891 time to fit residues: 7.7320 Evaluate side-chains 53 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 57 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 133 optimal weight: 0.0770 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 146 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 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 = 0.3830 r_free = 0.3830 target = 0.072170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.043095 restraints weight = 146996.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.042156 restraints weight = 127642.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.042267 restraints weight = 107372.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.041874 restraints weight = 90246.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.041718 restraints weight = 88164.814| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12362 Z= 0.238 Angle : 0.795 10.001 16780 Z= 0.391 Chirality : 0.048 0.254 1880 Planarity : 0.005 0.060 2126 Dihedral : 12.008 119.216 2176 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.69 % Favored : 90.04 % Rotamer: Outliers : 1.25 % Allowed : 13.20 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.22), residues: 1476 helix: -1.38 (0.45), residues: 124 sheet: -1.15 (0.50), residues: 135 loop : -0.79 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 315 TYR 0.023 0.002 TYR A 138 PHE 0.012 0.002 PHE B 423 TRP 0.018 0.003 TRP A 86 HIS 0.009 0.002 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (12266) covalent geometry : angle 0.76268 / 0.38 (16560) SS BOND : bond 0.00530 / 0.34 ( 68) SS BOND : angle 1.48947 / 1.04 ( 136) hydrogen bonds : bond 0.03593 / 2.48 ( 165) hydrogen bonds : angle 7.52657 / 4.91 ( 342) link_ALPHA1-3 : bond 0.02042 / 0.98 ( 2) link_ALPHA1-3 : angle 2.74750 / 1.65 ( 6) link_BETA1-4 : bond 0.00355 / 0.21 ( 14) link_BETA1-4 : angle 3.08980 / 2.19 ( 42) link_NAG-ASN : bond 0.00677 / 0.44 ( 12) link_NAG-ASN : angle 2.52646 / 1.48 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7513 (mm) REVERT: A 474 MET cc_start: 0.9231 (mmp) cc_final: 0.8830 (mmm) REVERT: B 213 ASN cc_start: 0.9581 (m110) cc_final: 0.9164 (p0) REVERT: B 473 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9329 (pt) REVERT: B 474 MET cc_start: 0.9333 (mmm) cc_final: 0.8941 (mmm) outliers start: 17 outliers final: 12 residues processed: 54 average time/residue: 0.0927 time to fit residues: 8.1501 Evaluate side-chains 54 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 131 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 chunk 45 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 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 = 0.3826 r_free = 0.3826 target = 0.072098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.040841 restraints weight = 147914.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.040820 restraints weight = 127031.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040466 restraints weight = 109096.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.040285 restraints weight = 97423.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.040065 restraints weight = 97235.113| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12362 Z= 0.223 Angle : 0.768 10.238 16780 Z= 0.379 Chirality : 0.048 0.256 1880 Planarity : 0.004 0.051 2126 Dihedral : 11.730 118.735 2176 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.15 % Favored : 90.58 % Rotamer: Outliers : 1.11 % Allowed : 13.64 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1476 helix: -1.41 (0.45), residues: 124 sheet: -1.28 (0.51), residues: 125 loop : -0.84 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 238 TYR 0.021 0.002 TYR A 260 PHE 0.013 0.002 PHE B 423 TRP 0.019 0.002 TRP A 543 HIS 0.011 0.002 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (12266) covalent geometry : angle 0.73816 / 0.37 (16560) SS BOND : bond 0.00458 / 0.30 ( 68) SS BOND : angle 1.30980 / 0.90 ( 136) hydrogen bonds : bond 0.03281 / 2.30 ( 165) hydrogen bonds : angle 7.57985 / 4.94 ( 342) link_ALPHA1-3 : bond 0.01987 / 0.95 ( 2) link_ALPHA1-3 : angle 2.88783 / 1.74 ( 6) link_BETA1-4 : bond 0.00351 / 0.21 ( 14) link_BETA1-4 : angle 2.94171 / 2.07 ( 42) link_NAG-ASN : bond 0.00589 / 0.39 ( 12) link_NAG-ASN : angle 2.50584 / 1.47 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7544 (mm) REVERT: A 474 MET cc_start: 0.9214 (mmp) cc_final: 0.8804 (mmm) REVERT: B 213 ASN cc_start: 0.9620 (m110) cc_final: 0.9257 (p0) REVERT: B 389 ASP cc_start: 0.9267 (m-30) cc_final: 0.8983 (p0) REVERT: B 474 MET cc_start: 0.9334 (mmm) cc_final: 0.8924 (mmm) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.0906 time to fit residues: 7.6930 Evaluate side-chains 50 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 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 = 0.3875 r_free = 0.3875 target = 0.074447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.044288 restraints weight = 145214.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.043088 restraints weight = 118782.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.042790 restraints weight = 105126.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.042621 restraints weight = 91569.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.042630 restraints weight = 85542.405| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12362 Z= 0.124 Angle : 0.691 10.205 16780 Z= 0.333 Chirality : 0.048 0.251 1880 Planarity : 0.004 0.044 2126 Dihedral : 11.196 117.160 2176 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.27 % Favored : 91.46 % Rotamer: Outliers : 0.88 % Allowed : 13.94 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1476 helix: -1.32 (0.45), residues: 124 sheet: -1.29 (0.50), residues: 125 loop : -0.71 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 238 TYR 0.014 0.001 TYR A 672 PHE 0.009 0.002 PHE B 423 TRP 0.014 0.002 TRP A 543 HIS 0.007 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12266) covalent geometry : angle 0.66449 / 0.33 (16560) SS BOND : bond 0.00270 / 0.18 ( 68) SS BOND : angle 0.88527 / 0.61 ( 136) hydrogen bonds : bond 0.02804 / 1.92 ( 165) hydrogen bonds : angle 7.17495 / 4.70 ( 342) link_ALPHA1-3 : bond 0.02221 / 1.06 ( 2) link_ALPHA1-3 : angle 3.15810 / 1.91 ( 6) link_BETA1-4 : bond 0.00433 / 0.25 ( 14) link_BETA1-4 : angle 2.85307 / 1.98 ( 42) link_NAG-ASN : bond 0.00304 / 0.18 ( 12) link_NAG-ASN : angle 2.29981 / 1.36 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.03 seconds wall clock time: 74 minutes 34.29 seconds (4474.29 seconds total)