Starting phenix.real_space_refine on Sat Jul 4 03:50:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlu_24547/07_2026/7rlu_24547.map" } resolution = 2.9 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= 0.005 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 11508 2.51 5 N 3088 2.21 5 O 3484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18188 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "B" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "D" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "C" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4492 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 560} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'NAP': 1, 'PNS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'NAP': 1, 'PNS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 3.53, per 1000 atoms: 0.19 Number of scatterers: 18188 At special positions: 0 Unit cell: (99.56, 108.68, 117.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3484 8.00 N 3088 7.00 C 11508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 701.6 milliseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 49.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.606A pdb=" N LEU A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.761A pdb=" N SER A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 352' Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.702A pdb=" N VAL A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.918A pdb=" N VAL A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 457 through 474 Processing helix chain 'A' and resid 475 through 480 removed outlier: 4.092A pdb=" N LYS A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 514 through 521 removed outlier: 3.743A pdb=" N LYS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.981A pdb=" N SER A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.813A pdb=" N LEU A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 586 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 617 removed outlier: 3.524A pdb=" N LEU A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 4.074A pdb=" N GLN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 667 removed outlier: 3.807A pdb=" N HIS A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 removed outlier: 3.701A pdb=" N VAL A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 removed outlier: 3.514A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 769 removed outlier: 3.792A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.657A pdb=" N LYS A 802 " --> pdb=" O MET A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 829 removed outlier: 3.955A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 853 Processing helix chain 'A' and resid 886 through 892 removed outlier: 4.036A pdb=" N ASN A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 892' Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.620A pdb=" N LEU B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.764A pdb=" N SER B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 352' Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.718A pdb=" N VAL B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 381 removed outlier: 4.023A pdb=" N VAL B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 396 Processing helix chain 'B' and resid 457 through 474 Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.108A pdb=" N LYS B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.737A pdb=" N LYS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 537 removed outlier: 3.984A pdb=" N SER B 526 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 591 removed outlier: 3.788A pdb=" N LEU B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 583 " --> pdb=" O MET B 579 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 586 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 617 removed outlier: 3.524A pdb=" N LEU B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 4.085A pdb=" N GLN B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 removed outlier: 3.558A pdb=" N HIS B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 666 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 3.695A pdb=" N VAL B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.514A pdb=" N GLU B 729 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 769 removed outlier: 3.794A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 768 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 769 " --> pdb=" O GLY B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 removed outlier: 3.688A pdb=" N LYS B 802 " --> pdb=" O MET B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 829 removed outlier: 3.956A pdb=" N VAL B 823 " --> pdb=" O ASP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 853 Processing helix chain 'B' and resid 886 through 892 removed outlier: 4.034A pdb=" N ASN B 890 " --> pdb=" O GLU B 886 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 892' Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.624A pdb=" N LEU D 321 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.754A pdb=" N SER D 350 " --> pdb=" O ASP D 346 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 351 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 352 " --> pdb=" O PHE D 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 346 through 352' Processing helix chain 'D' and resid 353 through 368 removed outlier: 3.710A pdb=" N VAL D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 3.554A pdb=" N TYR D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 396 Processing helix chain 'D' and resid 457 through 474 Processing helix chain 'D' and resid 475 through 480 removed outlier: 4.089A pdb=" N LYS D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 499 Processing helix chain 'D' and resid 499 through 511 Processing helix chain 'D' and resid 514 through 521 removed outlier: 3.749A pdb=" N LYS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 537 removed outlier: 3.981A pdb=" N SER D 526 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 536 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 591 removed outlier: 3.789A pdb=" N LEU D 580 " --> pdb=" O PRO D 576 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 583 " --> pdb=" O MET D 579 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 586 " --> pdb=" O TRP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 617 removed outlier: 3.525A pdb=" N LEU D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS D 615 " --> pdb=" O GLU D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 4.084A pdb=" N GLN D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 667 removed outlier: 3.550A pdb=" N HIS D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN D 666 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 700 removed outlier: 3.703A pdb=" N VAL D 699 " --> pdb=" O GLY D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 734 removed outlier: 3.509A pdb=" N GLU D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 733 " --> pdb=" O GLU D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 769 removed outlier: 3.796A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 768 " --> pdb=" O ARG D 764 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 803 removed outlier: 3.667A pdb=" N LYS D 802 " --> pdb=" O MET D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 829 removed outlier: 3.959A pdb=" N VAL D 823 " --> pdb=" O ASP D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 853 Processing helix chain 'D' and resid 886 through 892 removed outlier: 4.011A pdb=" N ASN D 890 " --> pdb=" O GLU D 886 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 891 " --> pdb=" O ALA D 887 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR D 892 " --> pdb=" O ALA D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 892' Processing helix chain 'C' and resid 317 through 335 removed outlier: 3.610A pdb=" N LEU C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.756A pdb=" N SER C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 351 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 352' Processing helix chain 'C' and resid 353 through 368 removed outlier: 3.710A pdb=" N VAL C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 381 removed outlier: 4.015A pdb=" N VAL C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 396 Processing helix chain 'C' and resid 457 through 474 Processing helix chain 'C' and resid 475 through 480 removed outlier: 4.090A pdb=" N LYS C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 499 Processing helix chain 'C' and resid 499 through 511 Processing helix chain 'C' and resid 514 through 521 removed outlier: 3.745A pdb=" N LYS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.978A pdb=" N SER C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 536 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 537 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 591 removed outlier: 3.811A pdb=" N LEU C 580 " --> pdb=" O PRO C 576 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 583 " --> pdb=" O MET C 579 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA C 586 " --> pdb=" O TRP C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 617 removed outlier: 3.525A pdb=" N LEU C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 640 removed outlier: 4.076A pdb=" N GLN C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 638 " --> pdb=" O GLY C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 667 removed outlier: 3.567A pdb=" N HIS C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 658 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 666 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 700 removed outlier: 3.708A pdb=" N VAL C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.515A pdb=" N GLU C 729 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 733 " --> pdb=" O GLU C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 769 removed outlier: 3.792A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 768 " --> pdb=" O ARG C 764 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 803 removed outlier: 3.720A pdb=" N LYS C 802 " --> pdb=" O MET C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 829 removed outlier: 3.962A pdb=" N VAL C 823 " --> pdb=" O ASP C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 853 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.028A pdb=" N ASN C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 removed outlier: 3.572A pdb=" N VAL A 431 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 442 removed outlier: 4.320A pdb=" N CYS A 451 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.785A pdb=" N ALA A 543 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 557 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL B 858 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR A 897 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE B 860 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 899 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER B 678 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 711 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N SER B 813 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 713 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 815 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 715 " --> pdb=" O PHE B 815 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 790 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.969A pdb=" N VAL A 566 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 645 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 644 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N SER A 671 " --> pdb=" O ARG A 644 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 646 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 771 through 774 removed outlier: 6.898A pdb=" N VAL A 790 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY A 711 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER A 813 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 713 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 815 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 715 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER A 678 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 557 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 543 " --> pdb=" O THR B 559 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 424 through 425 removed outlier: 3.575A pdb=" N VAL B 431 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 438 through 442 removed outlier: 4.316A pdb=" N CYS B 451 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 623 through 625 removed outlier: 6.967A pdb=" N VAL B 566 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 645 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 644 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N SER B 671 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 646 " --> pdb=" O SER B 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB3, first strand: chain 'D' and resid 424 through 425 removed outlier: 3.571A pdb=" N VAL D 431 " --> pdb=" O LEU D 424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 438 through 442 removed outlier: 4.317A pdb=" N CYS D 451 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 543 through 545 removed outlier: 3.787A pdb=" N ALA D 543 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR D 557 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL C 858 " --> pdb=" O ILE D 895 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR D 897 " --> pdb=" O VAL C 858 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE C 860 " --> pdb=" O THR D 897 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR D 899 " --> pdb=" O ILE C 860 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER C 678 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY C 711 " --> pdb=" O ILE C 809 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE C 811 " --> pdb=" O GLY C 711 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C 790 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 623 through 625 removed outlier: 6.966A pdb=" N VAL D 566 " --> pdb=" O VAL D 643 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 645 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG D 644 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N SER D 671 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE D 646 " --> pdb=" O SER D 671 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 771 through 774 removed outlier: 6.903A pdb=" N VAL D 790 " --> pdb=" O VAL D 773 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY D 711 " --> pdb=" O ILE D 811 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N SER D 813 " --> pdb=" O GLY D 711 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 713 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 815 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 715 " --> pdb=" O PHE D 815 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER D 678 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 557 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 543 " --> pdb=" O THR C 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 410 through 413 Processing sheet with id=AB9, first strand: chain 'C' and resid 424 through 425 removed outlier: 3.572A pdb=" N VAL C 431 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 438 through 442 removed outlier: 4.321A pdb=" N CYS C 451 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 623 through 625 removed outlier: 6.963A pdb=" N VAL C 566 " --> pdb=" O VAL C 643 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 645 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG C 644 " --> pdb=" O LYS C 669 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N SER C 671 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 646 " --> pdb=" O SER C 671 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2502 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: 3.09 Time building geometry restraints manager: 1.78 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: 5335 1.34 - 1.46: 2476 1.46 - 1.58: 10517 1.58 - 1.70: 16 1.70 - 1.82: 148 Bond restraints: 18492 Sorted by residual: bond pdb=" O3 NAP B1001 " pdb=" PA NAP B1001 " ideal model delta sigma weight residual 1.647 1.510 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" O3 NAP D1001 " pdb=" PA NAP D1001 " ideal model delta sigma weight residual 1.647 1.510 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O2B NAP A1001 " pdb=" P2B NAP A1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O2B NAP C1001 " pdb=" P2B NAP C1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O2B NAP D1001 " pdb=" P2B NAP D1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 18487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 23931 2.98 - 5.96: 1091 5.96 - 8.94: 14 8.94 - 11.92: 4 11.92 - 14.90: 4 Bond angle restraints: 25044 Sorted by residual: angle pdb=" O2A NAP D1001 " pdb=" PA NAP D1001 " pdb=" O3 NAP D1001 " ideal model delta sigma weight residual 104.94 119.84 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O2A NAP B1001 " pdb=" PA NAP B1001 " pdb=" O3 NAP B1001 " ideal model delta sigma weight residual 104.94 119.82 -14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O1A NAP D1001 " pdb=" PA NAP D1001 " pdb=" O2A NAP D1001 " ideal model delta sigma weight residual 121.77 108.05 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" O1A NAP B1001 " pdb=" PA NAP B1001 " pdb=" O2A NAP B1001 " ideal model delta sigma weight residual 121.77 108.09 13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" C VAL C 654 " pdb=" N GLY C 655 " pdb=" CA GLY C 655 " ideal model delta sigma weight residual 119.98 124.34 -4.36 1.11e+00 8.12e-01 1.54e+01 ... (remaining 25039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 10067 16.23 - 32.46: 745 32.46 - 48.69: 198 48.69 - 64.91: 34 64.91 - 81.14: 12 Dihedral angle restraints: 11056 sinusoidal: 4396 harmonic: 6660 Sorted by residual: dihedral pdb=" CA PRO B 603 " pdb=" C PRO B 603 " pdb=" N LEU B 604 " pdb=" CA LEU B 604 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 603 " pdb=" C PRO A 603 " pdb=" N LEU A 604 " pdb=" CA LEU A 604 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO C 603 " pdb=" C PRO C 603 " pdb=" N LEU C 604 " pdb=" CA LEU C 604 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1250 0.043 - 0.085: 835 0.085 - 0.128: 618 0.128 - 0.170: 137 0.170 - 0.213: 8 Chirality restraints: 2848 Sorted by residual: chirality pdb=" C2B NAP B1001 " pdb=" C1B NAP B1001 " pdb=" C3B NAP B1001 " pdb=" O2B NAP B1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C2B NAP D1001 " pdb=" C1B NAP D1001 " pdb=" C3B NAP D1001 " pdb=" O2B NAP D1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C2B NAP A1001 " pdb=" C1B NAP A1001 " pdb=" C3B NAP A1001 " pdb=" O2B NAP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2845 not shown) Planarity restraints: 3224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1003 " -0.037 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" C34 PNS B1003 " 0.026 2.00e-02 2.50e+03 pdb=" C37 PNS B1003 " -0.043 2.00e-02 2.50e+03 pdb=" N36 PNS B1003 " 0.051 2.00e-02 2.50e+03 pdb=" O35 PNS B1003 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 531 " 0.187 9.50e-02 1.11e+02 8.41e-02 4.36e+00 pdb=" NE ARG B 531 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 531 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 531 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 531 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 531 " -0.187 9.50e-02 1.11e+02 8.40e-02 4.36e+00 pdb=" NE ARG C 531 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 531 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 531 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 531 " -0.006 2.00e-02 2.50e+03 ... (remaining 3221 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 8773 3.05 - 3.51: 18542 3.51 - 3.97: 28779 3.97 - 4.44: 33403 4.44 - 4.90: 55427 Nonbonded interactions: 144924 Sorted by model distance: nonbonded pdb=" O ALA A 610 " pdb=" OG1 THR A 613 " model vdw 2.582 3.040 nonbonded pdb=" O ALA C 610 " pdb=" OG1 THR C 613 " model vdw 2.583 3.040 nonbonded pdb=" O ALA B 610 " pdb=" OG1 THR B 613 " model vdw 2.584 3.040 nonbonded pdb=" O ALA D 610 " pdb=" OG1 THR D 613 " model vdw 2.584 3.040 nonbonded pdb=" O MET B 525 " pdb=" OG1 THR B 529 " model vdw 2.600 3.040 ... (remaining 144919 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' and resid 313 through 1001) selection = (chain 'B' and resid 313 through 1001) selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.460 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.009 0.137 18500 Z= 0.656 Angle : 1.276 14.900 25044 Z= 0.859 Chirality : 0.069 0.213 2848 Planarity : 0.005 0.084 3224 Dihedral : 12.926 81.142 6776 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.31 % Favored : 94.00 % Rotamer: Outliers : 0.31 % Allowed : 3.78 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.29 (0.13), residues: 2316 helix: -0.97 (0.13), residues: 912 sheet: -3.37 (0.19), residues: 408 loop : -2.74 (0.15), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 531 TYR 0.010 0.001 TYR A 490 PHE 0.012 0.001 PHE D 839 TRP 0.006 0.001 TRP A 582 HIS 0.004 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00939 / 0.65 (18492) covalent geometry : angle 1.27616 / 0.86 (25044) hydrogen bonds : bond 0.30525 / 20.37 ( 847) hydrogen bonds : angle 8.16436 / 5.82 ( 2502) Misc. bond : bond 0.04941 / 3.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 412 time to evaluate : 0.486 Fit side-chains REVERT: A 738 ASN cc_start: 0.8039 (t0) cc_final: 0.7799 (t0) REVERT: B 738 ASN cc_start: 0.8016 (t0) cc_final: 0.7788 (t0) REVERT: D 738 ASN cc_start: 0.7995 (t0) cc_final: 0.7756 (t0) REVERT: C 738 ASN cc_start: 0.8013 (t0) cc_final: 0.7770 (t0) outliers start: 6 outliers final: 0 residues processed: 418 average time/residue: 0.6579 time to fit residues: 301.9496 Evaluate side-chains 230 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN A 749 GLN A 844 ASN B 414 ASN B 474 ASN B 749 GLN B 844 ASN D 414 ASN D 749 GLN D 844 ASN C 414 ASN C 749 GLN C 844 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.170235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133478 restraints weight = 17557.018| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.56 r_work: 0.3289 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18500 Z= 0.119 Angle : 0.519 8.701 25044 Z= 0.282 Chirality : 0.040 0.178 2848 Planarity : 0.003 0.028 3224 Dihedral : 5.654 48.571 2536 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 1.35 % Allowed : 12.01 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.01 (0.16), residues: 2316 helix: 1.16 (0.15), residues: 980 sheet: -2.18 (0.22), residues: 420 loop : -1.93 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 359 TYR 0.006 0.001 TYR B 902 PHE 0.019 0.002 PHE C 900 TRP 0.006 0.001 TRP D 573 HIS 0.004 0.001 HIS B 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (18492) covalent geometry : angle 0.51932 / 0.28 (25044) hydrogen bonds : bond 0.03989 / 2.64 ( 847) hydrogen bonds : angle 4.31175 / 3.15 ( 2502) Misc. bond : bond 0.00050 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 0.608 Fit side-chains REVERT: A 332 MET cc_start: 0.7651 (mmm) cc_final: 0.7405 (mmm) REVERT: A 342 GLU cc_start: 0.7699 (pt0) cc_final: 0.7374 (pt0) REVERT: A 554 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7735 (mtt-85) REVERT: A 732 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7044 (mt-10) REVERT: B 332 MET cc_start: 0.7590 (mmm) cc_final: 0.7368 (mmm) REVERT: B 342 GLU cc_start: 0.7653 (pt0) cc_final: 0.7345 (pt0) REVERT: B 554 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7632 (mtt-85) REVERT: B 732 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7065 (mt-10) REVERT: D 332 MET cc_start: 0.7645 (mmm) cc_final: 0.7428 (mmm) REVERT: D 554 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7739 (mtt-85) REVERT: D 732 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7067 (mt-10) REVERT: C 332 MET cc_start: 0.7627 (mmm) cc_final: 0.7412 (mmm) REVERT: C 554 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7655 (mtt-85) REVERT: C 732 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7037 (mt-10) outliers start: 26 outliers final: 1 residues processed: 328 average time/residue: 0.6620 time to fit residues: 239.0122 Evaluate side-chains 223 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 37 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 GLN ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.161767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126437 restraints weight = 17856.404| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.51 r_work: 0.3121 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 18500 Z= 0.304 Angle : 0.729 7.029 25044 Z= 0.386 Chirality : 0.049 0.196 2848 Planarity : 0.006 0.045 3224 Dihedral : 6.667 52.732 2536 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.54 % Favored : 96.29 % Rotamer: Outliers : 2.85 % Allowed : 12.94 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.13 (0.16), residues: 2316 helix: 0.53 (0.15), residues: 1004 sheet: -1.72 (0.21), residues: 448 loop : -1.64 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 712 TYR 0.016 0.003 TYR C 892 PHE 0.019 0.003 PHE A 875 TRP 0.015 0.003 TRP B 477 HIS 0.010 0.003 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.30 (18492) covalent geometry : angle 0.72875 / 0.39 (25044) hydrogen bonds : bond 0.06920 / 4.55 ( 847) hydrogen bonds : angle 4.68431 / 3.39 ( 2502) Misc. bond : bond 0.00172 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.451 Fit side-chains REVERT: A 332 MET cc_start: 0.7913 (mmm) cc_final: 0.7712 (mmm) REVERT: A 342 GLU cc_start: 0.7967 (pt0) cc_final: 0.7642 (pt0) REVERT: A 487 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8610 (tpm-80) REVERT: A 644 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8244 (mmp80) REVERT: A 781 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6284 (ttm-80) REVERT: A 891 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: A 901 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: B 332 MET cc_start: 0.7905 (mmm) cc_final: 0.7698 (mmm) REVERT: B 342 GLU cc_start: 0.8023 (pt0) cc_final: 0.7641 (pt0) REVERT: B 487 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8609 (tpm-80) REVERT: B 644 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8305 (mmp80) REVERT: B 725 GLN cc_start: 0.8027 (tp40) cc_final: 0.7537 (tt0) REVERT: B 781 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6297 (ttm-80) REVERT: B 891 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: D 342 GLU cc_start: 0.7734 (pt0) cc_final: 0.7202 (pt0) REVERT: D 487 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8606 (tpm-80) REVERT: D 644 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8327 (mmp80) REVERT: D 725 GLN cc_start: 0.8089 (tp40) cc_final: 0.7594 (tt0) REVERT: D 781 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6293 (ttm-80) REVERT: C 342 GLU cc_start: 0.7714 (pt0) cc_final: 0.7154 (pt0) REVERT: C 487 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (tpm-80) REVERT: C 494 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8273 (m-30) REVERT: C 644 ARG cc_start: 0.8544 (mtp85) cc_final: 0.8289 (mmp80) REVERT: C 725 GLN cc_start: 0.8003 (tp40) cc_final: 0.7515 (tt0) REVERT: C 781 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6287 (ttm-80) REVERT: C 891 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: C 901 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8342 (tp30) outliers start: 55 outliers final: 13 residues processed: 275 average time/residue: 0.7633 time to fit residues: 228.9408 Evaluate side-chains 226 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 487 ARG Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 781 ARG Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 901 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 178 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 738 ASN A 745 ASN B 738 ASN B 745 ASN D 738 ASN D 877 GLN C 635 GLN C 738 ASN C 745 ASN C 877 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.166199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.132278 restraints weight = 17725.025| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.66 r_work: 0.3198 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18500 Z= 0.128 Angle : 0.514 5.215 25044 Z= 0.279 Chirality : 0.041 0.183 2848 Planarity : 0.004 0.042 3224 Dihedral : 6.002 48.320 2536 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 2.17 % Allowed : 14.86 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.33 (0.17), residues: 2316 helix: 1.17 (0.16), residues: 1016 sheet: -1.01 (0.24), residues: 412 loop : -1.42 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 781 TYR 0.009 0.001 TYR D 490 PHE 0.023 0.002 PHE D 648 TRP 0.009 0.001 TRP B 477 HIS 0.005 0.001 HIS B 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (18492) covalent geometry : angle 0.51397 / 0.28 (25044) hydrogen bonds : bond 0.04152 / 2.74 ( 847) hydrogen bonds : angle 4.13868 / 3.02 ( 2502) Misc. bond : bond 0.00079 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.551 Fit side-chains REVERT: A 332 MET cc_start: 0.7728 (mmm) cc_final: 0.7476 (mmm) REVERT: B 332 MET cc_start: 0.7718 (mmm) cc_final: 0.7508 (mmm) REVERT: B 342 GLU cc_start: 0.7878 (pt0) cc_final: 0.7610 (pt0) REVERT: D 332 MET cc_start: 0.7819 (mmm) cc_final: 0.7570 (mmm) REVERT: D 342 GLU cc_start: 0.7659 (pt0) cc_final: 0.7154 (pt0) REVERT: D 725 GLN cc_start: 0.8072 (tp40) cc_final: 0.7526 (tt0) REVERT: C 332 MET cc_start: 0.7824 (mmm) cc_final: 0.7579 (mmm) REVERT: C 342 GLU cc_start: 0.7666 (pt0) cc_final: 0.7166 (pt0) REVERT: C 494 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: C 551 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7582 (mtp180) outliers start: 42 outliers final: 7 residues processed: 262 average time/residue: 0.7993 time to fit residues: 228.2399 Evaluate side-chains 209 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 673 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 139 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 121 optimal weight: 0.0020 chunk 82 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 635 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.166405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.134179 restraints weight = 17677.302| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.48 r_work: 0.3238 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18500 Z= 0.105 Angle : 0.479 5.584 25044 Z= 0.257 Chirality : 0.039 0.144 2848 Planarity : 0.004 0.039 3224 Dihedral : 5.635 46.975 2536 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 1.19 % Allowed : 17.65 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.16 (0.17), residues: 2316 helix: 1.55 (0.16), residues: 1016 sheet: -0.65 (0.24), residues: 452 loop : -1.22 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 781 TYR 0.008 0.001 TYR A 515 PHE 0.017 0.001 PHE D 648 TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (18492) covalent geometry : angle 0.47863 / 0.26 (25044) hydrogen bonds : bond 0.03517 / 2.33 ( 847) hydrogen bonds : angle 3.91567 / 2.87 ( 2502) Misc. bond : bond 0.00054 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.653 Fit side-chains REVERT: A 417 THR cc_start: 0.8526 (t) cc_final: 0.8272 (m) REVERT: A 554 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7696 (mtt-85) REVERT: A 560 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8518 (mttt) REVERT: A 781 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.5901 (ttm-80) REVERT: A 793 ASP cc_start: 0.8035 (t0) cc_final: 0.7807 (t0) REVERT: B 342 GLU cc_start: 0.7754 (pt0) cc_final: 0.7479 (pt0) REVERT: B 417 THR cc_start: 0.8509 (t) cc_final: 0.8262 (m) REVERT: B 560 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: B 781 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.5859 (ttm-80) REVERT: B 793 ASP cc_start: 0.8040 (t0) cc_final: 0.7819 (t0) REVERT: B 876 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6338 (pttt) REVERT: D 332 MET cc_start: 0.7629 (mmm) cc_final: 0.7353 (mmm) REVERT: D 342 GLU cc_start: 0.7564 (pt0) cc_final: 0.7089 (pt0) REVERT: D 417 THR cc_start: 0.8521 (t) cc_final: 0.8277 (m) REVERT: D 560 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8523 (mttp) REVERT: D 781 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.5851 (ttm-80) REVERT: D 793 ASP cc_start: 0.8062 (t0) cc_final: 0.7817 (t0) REVERT: C 332 MET cc_start: 0.7663 (mmm) cc_final: 0.7396 (mmm) REVERT: C 342 GLU cc_start: 0.7470 (pt0) cc_final: 0.6990 (pt0) REVERT: C 417 THR cc_start: 0.8566 (t) cc_final: 0.8283 (m) REVERT: C 494 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: C 560 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8511 (mttp) REVERT: C 781 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.5894 (ttm-80) outliers start: 23 outliers final: 5 residues processed: 243 average time/residue: 0.7511 time to fit residues: 199.3340 Evaluate side-chains 217 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 876 LYS Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 781 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 0.0570 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 121 optimal weight: 0.0070 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN A 738 ASN B 635 GLN B 738 ASN D 738 ASN C 414 ASN C 635 GLN C 738 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.168915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.134156 restraints weight = 17633.491| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.53 r_work: 0.3229 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18500 Z= 0.098 Angle : 0.459 5.739 25044 Z= 0.249 Chirality : 0.039 0.150 2848 Planarity : 0.003 0.038 3224 Dihedral : 5.461 46.072 2536 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 1.97 % Allowed : 17.49 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.42 (0.18), residues: 2316 helix: 1.75 (0.16), residues: 1016 sheet: -0.32 (0.25), residues: 456 loop : -1.19 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 781 TYR 0.008 0.001 TYR A 515 PHE 0.015 0.001 PHE C 815 TRP 0.007 0.001 TRP A 477 HIS 0.003 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (18492) covalent geometry : angle 0.45865 / 0.25 (25044) hydrogen bonds : bond 0.03239 / 2.15 ( 847) hydrogen bonds : angle 3.81962 / 2.80 ( 2502) Misc. bond : bond 0.00047 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.731 Fit side-chains REVERT: A 414 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8163 (t0) REVERT: A 417 THR cc_start: 0.8440 (t) cc_final: 0.8228 (m) REVERT: A 554 ARG cc_start: 0.8376 (mtm110) cc_final: 0.7702 (mtt-85) REVERT: A 560 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8616 (mttt) REVERT: A 781 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.5748 (ttm-80) REVERT: A 793 ASP cc_start: 0.8049 (t0) cc_final: 0.7783 (t0) REVERT: B 342 GLU cc_start: 0.7768 (pt0) cc_final: 0.7496 (pt0) REVERT: B 417 THR cc_start: 0.8398 (t) cc_final: 0.8190 (m) REVERT: B 560 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (mttp) REVERT: B 781 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.5716 (ttm-80) REVERT: B 793 ASP cc_start: 0.8045 (t0) cc_final: 0.7778 (t0) REVERT: D 332 MET cc_start: 0.7578 (mmm) cc_final: 0.7364 (mmm) REVERT: D 342 GLU cc_start: 0.7422 (pt0) cc_final: 0.7026 (pt0) REVERT: D 417 THR cc_start: 0.8407 (t) cc_final: 0.8199 (m) REVERT: D 554 ARG cc_start: 0.8351 (mtm110) cc_final: 0.7685 (mtt-85) REVERT: D 560 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8597 (mttp) REVERT: D 725 GLN cc_start: 0.8050 (tp40) cc_final: 0.7427 (tt0) REVERT: D 781 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.5711 (ttm-80) REVERT: D 793 ASP cc_start: 0.8092 (t0) cc_final: 0.7821 (t0) REVERT: C 332 MET cc_start: 0.7612 (mmm) cc_final: 0.7385 (mmm) REVERT: C 342 GLU cc_start: 0.7192 (pt0) cc_final: 0.6722 (pt0) REVERT: C 414 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (t0) REVERT: C 417 THR cc_start: 0.8508 (t) cc_final: 0.8285 (m) REVERT: C 494 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: C 551 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7523 (mtp180) REVERT: C 560 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: C 781 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.5727 (ttm-80) outliers start: 38 outliers final: 5 residues processed: 246 average time/residue: 0.7390 time to fit residues: 199.9834 Evaluate side-chains 215 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 781 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN A 522 HIS B 522 HIS B 635 GLN C 414 ASN C 635 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.164765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.130194 restraints weight = 17624.053| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.62 r_work: 0.3161 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18500 Z= 0.168 Angle : 0.542 4.948 25044 Z= 0.291 Chirality : 0.042 0.146 2848 Planarity : 0.004 0.040 3224 Dihedral : 6.055 50.511 2536 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.55 % Allowed : 18.12 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.12 (0.17), residues: 2316 helix: 1.31 (0.16), residues: 1024 sheet: -0.40 (0.24), residues: 460 loop : -1.13 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 781 TYR 0.008 0.002 TYR C 892 PHE 0.016 0.002 PHE C 815 TRP 0.010 0.002 TRP B 477 HIS 0.006 0.002 HIS B 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (18492) covalent geometry : angle 0.54229 / 0.29 (25044) hydrogen bonds : bond 0.04758 / 3.13 ( 847) hydrogen bonds : angle 4.16503 / 3.04 ( 2502) Misc. bond : bond 0.00097 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.698 Fit side-chains REVERT: A 380 MET cc_start: 0.7010 (mtp) cc_final: 0.6791 (mtm) REVERT: A 414 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 644 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8242 (mmp80) REVERT: A 781 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.5978 (ttm-80) REVERT: A 793 ASP cc_start: 0.8136 (t0) cc_final: 0.7901 (t0) REVERT: B 342 GLU cc_start: 0.7752 (pt0) cc_final: 0.7467 (pt0) REVERT: B 644 ARG cc_start: 0.8473 (mmp80) cc_final: 0.8240 (mmp80) REVERT: B 725 GLN cc_start: 0.7994 (tp40) cc_final: 0.7335 (tt0) REVERT: B 781 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.5949 (ttm-80) REVERT: B 793 ASP cc_start: 0.8129 (t0) cc_final: 0.7879 (t0) REVERT: D 342 GLU cc_start: 0.7500 (pt0) cc_final: 0.7073 (pt0) REVERT: D 476 LEU cc_start: 0.8181 (tp) cc_final: 0.7829 (mt) REVERT: D 644 ARG cc_start: 0.8471 (mmp80) cc_final: 0.8238 (mmp80) REVERT: D 725 GLN cc_start: 0.8055 (tp40) cc_final: 0.7443 (tt0) REVERT: D 781 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.5962 (ttm-80) REVERT: D 793 ASP cc_start: 0.8135 (t0) cc_final: 0.7899 (t0) REVERT: C 342 GLU cc_start: 0.7388 (pt0) cc_final: 0.6878 (pt0) REVERT: C 414 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8385 (t0) REVERT: C 417 THR cc_start: 0.8525 (t) cc_final: 0.8294 (m) REVERT: C 494 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: C 551 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (mtp180) REVERT: C 644 ARG cc_start: 0.8492 (mmp80) cc_final: 0.8258 (mmp80) REVERT: C 725 GLN cc_start: 0.7984 (tp40) cc_final: 0.7316 (tt0) REVERT: C 781 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.5957 (ttm-80) outliers start: 30 outliers final: 6 residues processed: 232 average time/residue: 0.7280 time to fit residues: 185.0284 Evaluate side-chains 219 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 781 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 156 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 209 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN A 738 ASN B 738 ASN D 738 ASN C 414 ASN C 635 GLN C 738 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.168056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136198 restraints weight = 17702.844| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.35 r_work: 0.3253 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18500 Z= 0.096 Angle : 0.456 6.599 25044 Z= 0.247 Chirality : 0.039 0.153 2848 Planarity : 0.003 0.039 3224 Dihedral : 5.549 47.577 2536 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.24 % Allowed : 18.32 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.54 (0.18), residues: 2316 helix: 1.66 (0.16), residues: 1024 sheet: -0.06 (0.25), residues: 452 loop : -1.00 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 781 TYR 0.008 0.001 TYR D 515 PHE 0.016 0.001 PHE C 815 TRP 0.007 0.001 TRP B 477 HIS 0.003 0.001 HIS D 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (18492) covalent geometry : angle 0.45626 / 0.25 (25044) hydrogen bonds : bond 0.03183 / 2.12 ( 847) hydrogen bonds : angle 3.88021 / 2.85 ( 2502) Misc. bond : bond 0.00042 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.692 Fit side-chains REVERT: A 342 GLU cc_start: 0.7692 (pt0) cc_final: 0.7404 (pt0) REVERT: A 781 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.5844 (ttm-80) REVERT: A 793 ASP cc_start: 0.8002 (t0) cc_final: 0.7795 (t0) REVERT: B 342 GLU cc_start: 0.7710 (pt0) cc_final: 0.7452 (pt0) REVERT: B 725 GLN cc_start: 0.7971 (tp40) cc_final: 0.7388 (tt0) REVERT: B 781 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.5806 (ttm-80) REVERT: D 342 GLU cc_start: 0.7327 (pt0) cc_final: 0.6935 (pt0) REVERT: D 476 LEU cc_start: 0.8154 (tp) cc_final: 0.7845 (mt) REVERT: D 725 GLN cc_start: 0.8005 (tp40) cc_final: 0.7521 (tt0) REVERT: D 781 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.5784 (ttm-80) REVERT: D 793 ASP cc_start: 0.8058 (t0) cc_final: 0.7849 (t0) REVERT: C 342 GLU cc_start: 0.7109 (pt0) cc_final: 0.6811 (pt0) REVERT: C 414 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8386 (t0) REVERT: C 417 THR cc_start: 0.8443 (t) cc_final: 0.8215 (m) REVERT: C 494 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: C 551 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7528 (mtp180) REVERT: C 725 GLN cc_start: 0.7908 (tp40) cc_final: 0.7348 (tt0) REVERT: C 781 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.5846 (ttm-80) outliers start: 24 outliers final: 6 residues processed: 227 average time/residue: 0.7075 time to fit residues: 176.0994 Evaluate side-chains 211 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 781 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 188 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 GLN C 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.164326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131913 restraints weight = 17699.946| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.53 r_work: 0.3164 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18500 Z= 0.173 Angle : 0.551 6.525 25044 Z= 0.296 Chirality : 0.042 0.145 2848 Planarity : 0.004 0.042 3224 Dihedral : 6.142 51.505 2536 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.40 % Allowed : 18.94 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.14 (0.17), residues: 2316 helix: 1.27 (0.16), residues: 1020 sheet: -0.32 (0.24), residues: 460 loop : -1.06 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.008 0.002 TYR C 892 PHE 0.017 0.002 PHE C 815 TRP 0.010 0.002 TRP B 477 HIS 0.006 0.002 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (18492) covalent geometry : angle 0.55108 / 0.30 (25044) hydrogen bonds : bond 0.04839 / 3.19 ( 847) hydrogen bonds : angle 4.20061 / 3.06 ( 2502) Misc. bond : bond 0.00100 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.569 Fit side-chains REVERT: A 342 GLU cc_start: 0.7754 (pt0) cc_final: 0.7471 (pt0) REVERT: A 414 ASN cc_start: 0.8713 (t160) cc_final: 0.8366 (t0) REVERT: A 644 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8250 (mmp80) REVERT: A 781 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6025 (ttm-80) REVERT: A 793 ASP cc_start: 0.8188 (t0) cc_final: 0.7949 (t0) REVERT: B 342 GLU cc_start: 0.7788 (pt0) cc_final: 0.7507 (pt0) REVERT: B 644 ARG cc_start: 0.8477 (mmp80) cc_final: 0.8263 (mmp80) REVERT: B 725 GLN cc_start: 0.8028 (tp40) cc_final: 0.7469 (tt0) REVERT: B 735 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7675 (tttm) REVERT: B 781 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6003 (ttm-80) REVERT: D 342 GLU cc_start: 0.7485 (pt0) cc_final: 0.6990 (pt0) REVERT: D 476 LEU cc_start: 0.8210 (tp) cc_final: 0.7866 (mt) REVERT: D 644 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8254 (mmp80) REVERT: D 725 GLN cc_start: 0.8083 (tp40) cc_final: 0.7586 (tt0) REVERT: D 781 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6014 (ttm-80) REVERT: D 793 ASP cc_start: 0.8174 (t0) cc_final: 0.7942 (t0) REVERT: C 342 GLU cc_start: 0.7388 (pt0) cc_final: 0.7107 (pt0) REVERT: C 414 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8405 (t0) REVERT: C 417 THR cc_start: 0.8514 (t) cc_final: 0.8302 (m) REVERT: C 494 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: C 551 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7585 (mtp180) REVERT: C 644 ARG cc_start: 0.8478 (mmp80) cc_final: 0.8263 (mmp80) REVERT: C 725 GLN cc_start: 0.7991 (tp40) cc_final: 0.7456 (tt0) REVERT: C 735 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7632 (tttm) REVERT: C 781 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6003 (ttm-80) outliers start: 27 outliers final: 9 residues processed: 224 average time/residue: 0.7342 time to fit residues: 180.0086 Evaluate side-chains 217 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 781 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 93 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 154 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 738 ASN B 635 GLN D 738 ASN C 414 ASN C 738 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.166504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134734 restraints weight = 17760.555| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.47 r_work: 0.3213 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18500 Z= 0.122 Angle : 0.495 6.568 25044 Z= 0.268 Chirality : 0.040 0.154 2848 Planarity : 0.004 0.043 3224 Dihedral : 5.862 50.255 2536 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.14 % Allowed : 19.20 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.35 (0.17), residues: 2316 helix: 1.44 (0.16), residues: 1020 sheet: -0.17 (0.25), residues: 452 loop : -0.99 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 781 TYR 0.006 0.001 TYR C 902 PHE 0.017 0.001 PHE C 815 TRP 0.009 0.001 TRP B 477 HIS 0.004 0.001 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (18492) covalent geometry : angle 0.49533 / 0.27 (25044) hydrogen bonds : bond 0.03847 / 2.55 ( 847) hydrogen bonds : angle 4.03675 / 2.95 ( 2502) Misc. bond : bond 0.00065 / 0.04 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.673 Fit side-chains REVERT: A 342 GLU cc_start: 0.7696 (pt0) cc_final: 0.7398 (pt0) REVERT: A 414 ASN cc_start: 0.8676 (t160) cc_final: 0.8312 (t0) REVERT: A 476 LEU cc_start: 0.8196 (tp) cc_final: 0.7892 (mt) REVERT: A 644 ARG cc_start: 0.8471 (mmp80) cc_final: 0.8206 (mmp80) REVERT: A 781 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.5909 (ttm-80) REVERT: A 793 ASP cc_start: 0.8114 (t0) cc_final: 0.7892 (t0) REVERT: B 342 GLU cc_start: 0.7721 (pt0) cc_final: 0.7459 (pt0) REVERT: B 644 ARG cc_start: 0.8436 (mmp80) cc_final: 0.8166 (mmp80) REVERT: B 725 GLN cc_start: 0.7976 (tp40) cc_final: 0.7428 (tt0) REVERT: B 781 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.5886 (ttm-80) REVERT: D 342 GLU cc_start: 0.7399 (pt0) cc_final: 0.6988 (pt0) REVERT: D 476 LEU cc_start: 0.8173 (tp) cc_final: 0.7875 (mt) REVERT: D 644 ARG cc_start: 0.8464 (mmp80) cc_final: 0.8201 (mmp80) REVERT: D 725 GLN cc_start: 0.8006 (tp40) cc_final: 0.7541 (tt0) REVERT: D 781 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.5930 (ttm-80) REVERT: D 793 ASP cc_start: 0.8102 (t0) cc_final: 0.7865 (t0) REVERT: C 342 GLU cc_start: 0.7297 (pt0) cc_final: 0.7020 (pt0) REVERT: C 414 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8355 (t0) REVERT: C 417 THR cc_start: 0.8441 (t) cc_final: 0.8203 (m) REVERT: C 476 LEU cc_start: 0.8190 (tp) cc_final: 0.7816 (mt) REVERT: C 494 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: C 551 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7564 (mtp180) REVERT: C 644 ARG cc_start: 0.8478 (mmp80) cc_final: 0.8211 (mmp80) REVERT: C 725 GLN cc_start: 0.7941 (tp40) cc_final: 0.7405 (tt0) REVERT: C 735 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7485 (tttm) REVERT: C 781 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.5900 (ttm-80) outliers start: 22 outliers final: 10 residues processed: 206 average time/residue: 0.7638 time to fit residues: 172.4410 Evaluate side-chains 212 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 781 ARG Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 781 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 225 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 121 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 36 optimal weight: 0.0670 chunk 174 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.166740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.134400 restraints weight = 17882.749| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.42 r_work: 0.3256 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18500 Z= 0.091 Angle : 0.452 5.314 25044 Z= 0.246 Chirality : 0.038 0.142 2848 Planarity : 0.003 0.041 3224 Dihedral : 5.414 47.225 2536 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.04 % Allowed : 19.46 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.68 (0.18), residues: 2316 helix: 1.75 (0.16), residues: 1020 sheet: 0.02 (0.25), residues: 452 loop : -0.88 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 742 TYR 0.009 0.001 TYR B 515 PHE 0.016 0.001 PHE C 815 TRP 0.006 0.001 TRP C 477 HIS 0.002 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (18492) covalent geometry : angle 0.45211 / 0.25 (25044) hydrogen bonds : bond 0.02925 / 1.96 ( 847) hydrogen bonds : angle 3.82876 / 2.80 ( 2502) Misc. bond : bond 0.00035 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5854.90 seconds wall clock time: 100 minutes 35.12 seconds (6035.12 seconds total)