Starting phenix.real_space_refine (version: dev) on Sun May 15 11:38:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0m_13148/05_2022/7p0m_13148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0m_13148/05_2022/7p0m_13148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0m_13148/05_2022/7p0m_13148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0m_13148/05_2022/7p0m_13148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0m_13148/05_2022/7p0m_13148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p0m_13148/05_2022/7p0m_13148_updated.pdb" } resolution = 2.75 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.013 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 25185 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4159 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4181 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 25, 'TRANS': 510} Chain breaks: 1 Chain: "C" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4147 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 25, 'TRANS': 506} Chain breaks: 1 Chain: "D" Number of atoms: 4140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4140 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 24, 'TRANS': 506} Chain breaks: 1 Chain: "E" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4147 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 25, 'TRANS': 506} Chain breaks: 1 Chain: "F" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4054 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 25, 'TRANS': 494} Chain breaks: 3 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.41, per 1000 atoms: 0.57 Number of scatterers: 25185 At special positions: 0 Unit cell: (137.994, 128.184, 138.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 16 15.00 Mg 4 11.99 O 4819 8.00 N 4313 7.00 C 15913 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.05 Conformation dependent library (CDL) restraints added in 4.0 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5990 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 20 sheets defined 45.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.932A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.811A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.815A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.932A pdb=" N LYS A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.577A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 616 No H-bonds generated for 'chain 'A' and resid 613 through 616' Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.814A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 693 through 703 Processing helix chain 'A' and resid 710 through 729 Processing helix chain 'A' and resid 739 through 746 removed outlier: 4.805A pdb=" N GLN A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 746 " --> pdb=" O GLN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 removed outlier: 3.615A pdb=" N GLN A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 837 No H-bonds generated for 'chain 'A' and resid 834 through 837' Processing helix chain 'A' and resid 854 through 869 removed outlier: 4.563A pdb=" N CYS A 858 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 914 through 921 removed outlier: 4.723A pdb=" N LYS A 918 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 939 through 946 Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.257A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.614A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.542A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.813A pdb=" N ALA B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 603 through 610 removed outlier: 4.008A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.664A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 693 through 703 Processing helix chain 'B' and resid 710 through 729 Processing helix chain 'B' and resid 742 through 746 Processing helix chain 'B' and resid 808 through 828 Processing helix chain 'B' and resid 834 through 837 No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 854 through 869 removed outlier: 4.590A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 914 through 921 removed outlier: 4.657A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 928 No H-bonds generated for 'chain 'B' and resid 925 through 928' Processing helix chain 'B' and resid 939 through 946 removed outlier: 3.676A pdb=" N ASP B 944 " --> pdb=" O ARG B 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.634A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 480 through 490 removed outlier: 4.220A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 511 Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.763A pdb=" N ALA C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 603 through 610 removed outlier: 3.644A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 647 through 652 removed outlier: 3.554A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 removed outlier: 3.526A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 710 through 729 Processing helix chain 'C' and resid 742 through 746 Processing helix chain 'C' and resid 808 through 828 Processing helix chain 'C' and resid 834 through 837 No H-bonds generated for 'chain 'C' and resid 834 through 837' Processing helix chain 'C' and resid 854 through 869 removed outlier: 4.579A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 860 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 869 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 905 Processing helix chain 'C' and resid 914 through 921 removed outlier: 4.772A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 928 No H-bonds generated for 'chain 'C' and resid 925 through 928' Processing helix chain 'C' and resid 939 through 946 removed outlier: 3.640A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 427 removed outlier: 3.746A pdb=" N LEU D 425 " --> pdb=" O PHE D 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.951A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 467 removed outlier: 3.586A pdb=" N VAL D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 495 through 511 Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 556 through 559 No H-bonds generated for 'chain 'D' and resid 556 through 559' Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 603 through 611 Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 647 through 652 removed outlier: 3.753A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 674 through 682 Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 710 through 729 Processing helix chain 'D' and resid 742 through 746 removed outlier: 3.907A pdb=" N VAL D 746 " --> pdb=" O GLN D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.503A pdb=" N GLN D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 837 No H-bonds generated for 'chain 'D' and resid 834 through 837' Processing helix chain 'D' and resid 857 through 869 removed outlier: 3.579A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 905 removed outlier: 3.507A pdb=" N ILE D 900 " --> pdb=" O LYS D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 921 removed outlier: 4.589A pdb=" N LYS D 918 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 921 " --> pdb=" O LYS D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 928 No H-bonds generated for 'chain 'D' and resid 925 through 928' Processing helix chain 'D' and resid 939 through 946 removed outlier: 3.672A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 427 removed outlier: 3.530A pdb=" N LEU E 425 " --> pdb=" O PHE E 421 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 426 " --> pdb=" O ARG E 422 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 447 removed outlier: 4.132A pdb=" N ASP E 436 " --> pdb=" O LYS E 432 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 467 removed outlier: 3.761A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 490 Processing helix chain 'E' and resid 495 through 511 Processing helix chain 'E' and resid 529 through 539 removed outlier: 3.683A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 559 No H-bonds generated for 'chain 'E' and resid 556 through 559' Processing helix chain 'E' and resid 572 through 580 removed outlier: 3.645A pdb=" N LYS E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 647 through 652 removed outlier: 3.664A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 672 removed outlier: 3.634A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 681 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 729 Processing helix chain 'E' and resid 739 through 744 removed outlier: 3.528A pdb=" N LEU E 742 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.593A pdb=" N GLN E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 869 removed outlier: 4.617A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 867 " --> pdb=" O LEU E 864 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET E 869 " --> pdb=" O SER E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 921 removed outlier: 4.666A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR E 921 " --> pdb=" O LYS E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 928 No H-bonds generated for 'chain 'E' and resid 925 through 928' Processing helix chain 'E' and resid 939 through 946 removed outlier: 3.647A pdb=" N ASP E 944 " --> pdb=" O ARG E 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 427 removed outlier: 3.562A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 3.723A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 removed outlier: 4.067A pdb=" N VAL F 457 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG F 459 " --> pdb=" O PHE F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 490 Processing helix chain 'F' and resid 495 through 511 Processing helix chain 'F' and resid 529 through 539 removed outlier: 4.034A pdb=" N ALA F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 604 through 611 removed outlier: 3.846A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 616 No H-bonds generated for 'chain 'F' and resid 613 through 616' Processing helix chain 'F' and resid 647 through 650 No H-bonds generated for 'chain 'F' and resid 647 through 650' Processing helix chain 'F' and resid 663 through 672 removed outlier: 3.628A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 710 through 729 Processing helix chain 'F' and resid 742 through 746 Processing helix chain 'F' and resid 808 through 828 removed outlier: 3.776A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN F 827 " --> pdb=" O ALA F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 834 through 837 No H-bonds generated for 'chain 'F' and resid 834 through 837' Processing helix chain 'F' and resid 854 through 869 removed outlier: 4.686A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 867 " --> pdb=" O LEU F 864 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET F 869 " --> pdb=" O SER F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 914 through 921 removed outlier: 4.709A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 939 through 946 Processing sheet with id= A, first strand: chain 'A' and resid 654 through 658 removed outlier: 6.211A pdb=" N PHE A 635 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 521 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY A 523 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 639 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 634 " --> pdb=" O PRO A 585 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU A 543 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 588 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 764 through 769 Processing sheet with id= C, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.513A pdb=" N CYS A 909 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU A 932 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU A 912 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS A 934 " --> pdb=" O LEU A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 654 through 657 removed outlier: 3.638A pdb=" N GLU B 654 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE B 635 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE B 521 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 764 through 769 removed outlier: 6.156A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.522A pdb=" N CYS B 909 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU B 932 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 912 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N HIS B 934 " --> pdb=" O LEU B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 654 through 658 removed outlier: 6.027A pdb=" N PHE C 635 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE C 521 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N CYS C 637 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY C 523 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA C 639 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 634 " --> pdb=" O PRO C 585 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU C 543 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU C 588 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP C 590 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 547 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 764 through 769 removed outlier: 3.659A pdb=" N VAL C 844 " --> pdb=" O THR C 803 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.541A pdb=" N CYS C 909 " --> pdb=" O ALA C 878 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU C 932 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 912 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS C 934 " --> pdb=" O LEU C 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 654 through 658 removed outlier: 3.695A pdb=" N GLU D 654 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 635 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE D 521 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS D 637 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLY D 523 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA D 639 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU D 543 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU D 588 " --> pdb=" O GLU D 543 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 689 through 691 removed outlier: 7.149A pdb=" N VAL D 735 " --> pdb=" O LYS D 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 764 through 769 removed outlier: 6.194A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 877 through 879 removed outlier: 6.611A pdb=" N CYS D 909 " --> pdb=" O ALA D 878 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU D 932 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU D 912 " --> pdb=" O GLU D 932 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS D 934 " --> pdb=" O LEU D 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 654 through 657 removed outlier: 3.524A pdb=" N GLU E 654 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE E 635 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE E 521 " --> pdb=" O PHE E 635 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS E 637 " --> pdb=" O PHE E 521 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.022A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 764 through 770 Processing sheet with id= Q, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.480A pdb=" N CYS E 909 " --> pdb=" O ALA E 878 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU E 932 " --> pdb=" O ILE E 910 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU E 912 " --> pdb=" O GLU E 932 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS E 934 " --> pdb=" O LEU E 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 653 through 658 removed outlier: 6.957A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL F 658 " --> pdb=" O CYS F 520 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR F 522 " --> pdb=" O VAL F 658 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU F 543 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU F 588 " --> pdb=" O GLU F 543 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 764 through 771 removed outlier: 3.828A pdb=" N VAL F 844 " --> pdb=" O THR F 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.520A pdb=" N CYS F 909 " --> pdb=" O ALA F 878 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 958 hydrogen bonds defined for protein. 2592 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: 8.84 Time building geometry restraints manager: 11.70 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: 8332 1.34 - 1.46: 3622 1.46 - 1.58: 13454 1.58 - 1.70: 25 1.70 - 1.82: 198 Bond restraints: 25631 Sorted by residual: bond pdb=" N MET F 569 " pdb=" CA MET F 569 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.50e-02 4.44e+03 5.43e+00 bond pdb=" N GLU F 781 " pdb=" CA GLU F 781 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.21e-02 6.83e+03 5.32e+00 bond pdb=" C MET F 569 " pdb=" N PRO F 570 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.25e-02 6.40e+03 2.71e+00 bond pdb=" C PRO F 570 " pdb=" O PRO F 570 " ideal model delta sigma weight residual 1.233 1.217 0.016 1.12e-02 7.97e+03 2.14e+00 bond pdb=" CA PRO F 570 " pdb=" C PRO F 570 " ideal model delta sigma weight residual 1.520 1.535 -0.016 1.24e-02 6.50e+03 1.63e+00 ... (remaining 25626 not shown) Histogram of bond angle deviations from ideal: 100.17 - 108.11: 1028 108.11 - 116.05: 16202 116.05 - 123.99: 16967 123.99 - 131.93: 479 131.93 - 139.86: 34 Bond angle restraints: 34710 Sorted by residual: angle pdb=" CB MET E 773 " pdb=" CG MET E 773 " pdb=" SD MET E 773 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CB MET A 435 " pdb=" CG MET A 435 " pdb=" SD MET A 435 " ideal model delta sigma weight residual 112.70 123.00 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB MET F 435 " pdb=" CG MET F 435 " pdb=" SD MET F 435 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N VAL D 555 " pdb=" CA VAL D 555 " pdb=" C VAL D 555 " ideal model delta sigma weight residual 113.39 109.14 4.25 1.47e+00 4.63e-01 8.34e+00 angle pdb=" CB MET C 655 " pdb=" CG MET C 655 " pdb=" SD MET C 655 " ideal model delta sigma weight residual 112.70 121.31 -8.61 3.00e+00 1.11e-01 8.24e+00 ... (remaining 34705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.82: 14563 26.82 - 53.64: 932 53.64 - 80.45: 69 80.45 - 107.27: 16 107.27 - 134.09: 2 Dihedral angle restraints: 15582 sinusoidal: 6293 harmonic: 9289 Sorted by residual: dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 165.91 134.09 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" O1B ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PB ADP E1001 " pdb=" PA ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 53.52 -113.52 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 46.86 -106.86 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 15579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2571 0.026 - 0.052: 812 0.052 - 0.079: 332 0.079 - 0.105: 180 0.105 - 0.131: 81 Chirality restraints: 3976 Sorted by residual: chirality pdb=" CA ILE A 645 " pdb=" N ILE A 645 " pdb=" C ILE A 645 " pdb=" CB ILE A 645 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE D 645 " pdb=" N ILE D 645 " pdb=" C ILE D 645 " pdb=" CB ILE D 645 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 645 " pdb=" N ILE B 645 " pdb=" C ILE B 645 " pdb=" CB ILE B 645 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 3973 not shown) Planarity restraints: 4451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 738 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 739 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 739 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 739 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 738 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO E 739 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 739 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 739 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 738 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.30e-01 pdb=" N PRO A 739 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 739 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 739 " 0.013 5.00e-02 4.00e+02 ... (remaining 4448 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 102 2.42 - 3.04: 15402 3.04 - 3.66: 38692 3.66 - 4.28: 59462 4.28 - 4.90: 97664 Nonbonded interactions: 211322 Sorted by model distance: nonbonded pdb=" OG SER E 855 " pdb=" C UNK K 390 " model vdw 1.800 3.270 nonbonded pdb=" OG SER A 855 " pdb=" C UNK I 390 " model vdw 1.834 3.270 nonbonded pdb=" OG SER E 855 " pdb=" O UNK K 390 " model vdw 1.846 2.440 nonbonded pdb=" CB SER B 855 " pdb=" C UNK H 390 " model vdw 1.855 3.670 nonbonded pdb=" OG SER A 855 " pdb=" O UNK I 390 " model vdw 1.870 2.440 ... (remaining 211317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 410 through 562 or resid 568 through 594 or resid 602 thro \ ugh 786 or resid 796 through 949)) selection = (chain 'B' and (resid 410 through 562 or resid 568 through 594 or resid 602 thro \ ugh 786 or resid 790 through 795 or resid 798 through 949)) selection = (chain 'C' and (resid 410 through 562 or resid 568 through 594 or resid 602 thro \ ugh 786 or resid 796 through 949)) selection = (chain 'D' and (resid 410 through 562 or resid 568 through 594 or resid 602 thro \ ugh 949)) selection = (chain 'E' and (resid 410 through 562 or resid 568 through 594 or resid 602 thro \ ugh 786 or resid 796 through 949)) selection = (chain 'F' and (resid 410 through 786 or resid 796 through 949)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 120 5.16 5 C 15913 2.51 5 N 4313 2.21 5 O 4819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 21.330 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: 0.000 Extract box with map and model: 39.170 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.200 Process input model: 71.150 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 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 : 0.002 0.036 25631 Z= 0.124 Angle : 0.440 11.605 34710 Z= 0.222 Chirality : 0.037 0.131 3976 Planarity : 0.002 0.040 4451 Dihedral : 16.307 134.088 9592 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3157 helix: 1.89 (0.13), residues: 1407 sheet: 1.66 (0.25), residues: 435 loop : 0.09 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 85 time to evaluate : 3.252 Fit side-chains outliers start: 51 outliers final: 40 residues processed: 136 average time/residue: 1.3020 time to fit residues: 210.9266 Evaluate side-chains 120 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 80 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 40 residues processed: 0 time to fit residues: 4.1425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.0170 chunk 133 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS D 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 25631 Z= 0.246 Angle : 0.488 7.052 34710 Z= 0.248 Chirality : 0.040 0.162 3976 Planarity : 0.004 0.076 4451 Dihedral : 5.492 124.305 3505 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.15), residues: 3157 helix: 1.87 (0.13), residues: 1436 sheet: 1.73 (0.25), residues: 419 loop : 0.06 (0.17), residues: 1302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 81 time to evaluate : 3.075 Fit side-chains outliers start: 84 outliers final: 47 residues processed: 155 average time/residue: 1.1840 time to fit residues: 219.9643 Evaluate side-chains 128 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 81 time to evaluate : 3.148 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 43 residues processed: 4 average time/residue: 1.1710 time to fit residues: 9.9718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 0.3980 chunk 312 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 25631 Z= 0.247 Angle : 0.482 9.490 34710 Z= 0.239 Chirality : 0.040 0.226 3976 Planarity : 0.004 0.046 4451 Dihedral : 5.465 115.771 3505 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.15), residues: 3157 helix: 1.74 (0.13), residues: 1433 sheet: 1.52 (0.25), residues: 419 loop : -0.01 (0.17), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 83 time to evaluate : 3.002 Fit side-chains outliers start: 92 outliers final: 48 residues processed: 167 average time/residue: 1.1221 time to fit residues: 226.0021 Evaluate side-chains 128 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 80 time to evaluate : 3.091 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 48 residues processed: 0 time to fit residues: 4.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.4980 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 25631 Z= 0.142 Angle : 0.443 8.399 34710 Z= 0.219 Chirality : 0.039 0.210 3976 Planarity : 0.003 0.076 4451 Dihedral : 5.272 113.927 3505 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 3157 helix: 1.82 (0.14), residues: 1432 sheet: 1.38 (0.25), residues: 423 loop : 0.05 (0.17), residues: 1302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 81 time to evaluate : 3.293 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 50 residues processed: 155 average time/residue: 1.2104 time to fit residues: 225.1692 Evaluate side-chains 132 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 82 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 49 residues processed: 1 average time/residue: 0.4287 time to fit residues: 4.8784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 228 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 chunk 262 optimal weight: 0.0870 chunk 212 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 275 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN F 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 25631 Z= 0.116 Angle : 0.436 9.470 34710 Z= 0.211 Chirality : 0.038 0.162 3976 Planarity : 0.003 0.047 4451 Dihedral : 5.061 115.173 3505 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.15), residues: 3157 helix: 1.91 (0.14), residues: 1434 sheet: 1.34 (0.25), residues: 431 loop : 0.07 (0.17), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 83 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 53 residues processed: 160 average time/residue: 1.1854 time to fit residues: 227.2845 Evaluate side-chains 133 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 80 time to evaluate : 3.075 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 52 residues processed: 1 average time/residue: 1.3995 time to fit residues: 5.7328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.0770 chunk 276 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.0170 chunk 75 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 25631 Z= 0.114 Angle : 0.442 13.331 34710 Z= 0.211 Chirality : 0.038 0.296 3976 Planarity : 0.003 0.047 4451 Dihedral : 4.946 118.032 3505 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.15), residues: 3157 helix: 1.94 (0.14), residues: 1444 sheet: 1.38 (0.25), residues: 432 loop : 0.08 (0.17), residues: 1281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 81 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 57 residues processed: 147 average time/residue: 1.2247 time to fit residues: 219.0841 Evaluate side-chains 138 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 81 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 54 residues processed: 3 average time/residue: 1.0054 time to fit residues: 7.7072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 174 optimal weight: 0.0370 chunk 259 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 306 optimal weight: 0.2980 chunk 191 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 25631 Z= 0.189 Angle : 0.472 13.139 34710 Z= 0.227 Chirality : 0.039 0.269 3976 Planarity : 0.003 0.086 4451 Dihedral : 5.009 121.980 3505 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.15), residues: 3157 helix: 1.92 (0.14), residues: 1441 sheet: 1.36 (0.25), residues: 420 loop : 0.04 (0.17), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 80 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 56 residues processed: 145 average time/residue: 1.2120 time to fit residues: 212.0801 Evaluate side-chains 137 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 81 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 56 residues processed: 0 time to fit residues: 4.2307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 59 optimal weight: 0.1980 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.069 25631 Z= 0.116 Angle : 0.455 11.986 34710 Z= 0.216 Chirality : 0.038 0.236 3976 Planarity : 0.003 0.058 4451 Dihedral : 4.843 121.204 3505 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3157 helix: 1.95 (0.14), residues: 1441 sheet: 1.31 (0.25), residues: 433 loop : 0.07 (0.17), residues: 1283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 82 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 56 residues processed: 148 average time/residue: 1.1494 time to fit residues: 207.6015 Evaluate side-chains 136 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 80 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 54 residues processed: 2 average time/residue: 0.8587 time to fit residues: 6.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 267 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 258 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 25631 Z= 0.125 Angle : 0.463 13.615 34710 Z= 0.217 Chirality : 0.038 0.226 3976 Planarity : 0.003 0.047 4451 Dihedral : 4.784 121.462 3505 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.15), residues: 3157 helix: 1.99 (0.14), residues: 1447 sheet: 1.30 (0.25), residues: 433 loop : 0.07 (0.17), residues: 1277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 81 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 54 residues processed: 139 average time/residue: 1.3421 time to fit residues: 223.4090 Evaluate side-chains 134 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 80 time to evaluate : 3.251 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 53 residues processed: 1 average time/residue: 1.4113 time to fit residues: 6.0750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 5.9990 chunk 302 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 316 optimal weight: 0.0870 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 25631 Z= 0.127 Angle : 0.469 14.290 34710 Z= 0.220 Chirality : 0.038 0.211 3976 Planarity : 0.003 0.047 4451 Dihedral : 4.708 121.285 3505 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.15), residues: 3157 helix: 1.99 (0.14), residues: 1448 sheet: 1.33 (0.25), residues: 431 loop : 0.07 (0.17), residues: 1278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 80 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 55 residues processed: 137 average time/residue: 1.2421 time to fit residues: 205.3365 Evaluate side-chains 135 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 80 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 53 residues processed: 2 average time/residue: 0.8533 time to fit residues: 6.2668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.033687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.027307 restraints weight = 183689.512| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.44 r_work: 0.2911 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work: 0.2898 rms_B_bonded: 2.23 restraints_weight: 0.1250 r_work: 0.2891 rms_B_bonded: 2.28 restraints_weight: 0.0625 r_work: 0.2884 rms_B_bonded: 2.35 restraints_weight: 0.0312 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.0156 r_work: 0.2869 rms_B_bonded: 2.56 restraints_weight: 0.0078 r_work: 0.2862 rms_B_bonded: 2.70 restraints_weight: 0.0039 r_work: 0.2854 rms_B_bonded: 2.85 restraints_weight: 0.0020 r_work: 0.2845 rms_B_bonded: 3.03 restraints_weight: 0.0010 r_work: 0.2837 rms_B_bonded: 3.23 restraints_weight: 0.0005 r_work: 0.2827 rms_B_bonded: 3.45 restraints_weight: 0.0002 r_work: 0.2818 rms_B_bonded: 3.69 restraints_weight: 0.0001 r_work: 0.2808 rms_B_bonded: 3.96 restraints_weight: 0.0001 r_work: 0.2797 rms_B_bonded: 4.26 restraints_weight: 0.0000 r_work: 0.2786 rms_B_bonded: 4.58 restraints_weight: 0.0000 r_work: 0.2775 rms_B_bonded: 4.94 restraints_weight: 0.0000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 25631 Z= 0.132 Angle : 0.462 13.724 34710 Z= 0.218 Chirality : 0.038 0.207 3976 Planarity : 0.003 0.047 4451 Dihedral : 4.685 120.767 3505 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.15), residues: 3157 helix: 1.99 (0.14), residues: 1449 sheet: 1.32 (0.25), residues: 431 loop : 0.07 (0.17), residues: 1277 =============================================================================== Job complete usr+sys time: 5897.27 seconds wall clock time: 109 minutes 52.62 seconds (6592.62 seconds total)