Starting phenix.real_space_refine on Thu Jan 15 11:11:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p0m_13148/01_2026/7p0m_13148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p0m_13148/01_2026/7p0m_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 { model { file = "/net/cci-nas-00/data/ceres_data/7p0m_13148/01_2026/7p0m_13148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p0m_13148/01_2026/7p0m_13148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p0m_13148/01_2026/7p0m_13148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p0m_13148/01_2026/7p0m_13148.map" } 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 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= 0.001 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 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. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/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: 6.37, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 142 helices and 31 sheets defined 52.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.932A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.811A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.655A pdb=" N ASN A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 528 through 541 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 560 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 592 through 595 removed outlier: 3.504A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 592 through 595' Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.577A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 4.191A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.814A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.950A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 removed outlier: 3.615A pdb=" N GLN A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.866A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 431 through 448 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 452 through 468 removed outlier: 3.775A pdb=" N ASN B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 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) removed outlier: 3.716A pdb=" N HIS B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 528 through 541 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 554 through 558 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 602 through 611 removed outlier: 4.275A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.664A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 747 removed outlier: 3.872A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.866A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 944 " --> pdb=" O ARG B 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.634A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.827A pdb=" N ASN C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 4.220A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'C' and resid 528 through 541 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 554 through 558 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.685A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) 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 614 through 618 removed outlier: 3.910A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.554A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.526A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 removed outlier: 3.507A pdb=" N GLN C 677 " --> pdb=" O TYR C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 741 through 747 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 856 through 870 removed outlier: 3.586A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.885A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 425 removed outlier: 3.746A pdb=" N LEU D 425 " --> pdb=" O PHE D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 431 through 448 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 452 through 468 removed outlier: 3.693A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 530 through 541 removed outlier: 3.886A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 603 through 611 removed outlier: 3.556A pdb=" N LEU D 607 " --> pdb=" O PRO D 603 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 618 removed outlier: 3.734A pdb=" N ALA D 617 " --> pdb=" O GLU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.753A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 704 removed outlier: 3.787A pdb=" N CYS D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 730 Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 removed outlier: 3.503A pdb=" N GLN D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.579A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 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 916 through 922 Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.853A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) 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 428 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) removed outlier: 4.350A pdb=" N LEU E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 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 452 through 468 removed outlier: 3.876A pdb=" N ASN E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 528 through 540 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 555 through 560 removed outlier: 3.747A pdb=" N LYS E 559 " --> pdb=" O VAL E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 removed outlier: 3.645A pdb=" N LYS E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.502A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 653 removed outlier: 3.664A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 removed outlier: 3.634A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 682 Processing helix chain 'E' and resid 692 through 704 removed outlier: 3.764A pdb=" N CYS E 704 " --> pdb=" O ILE E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 730 Processing helix chain 'E' and resid 741 through 745 Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.593A pdb=" N GLN E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 853 through 855 No H-bonds generated for 'chain 'E' and resid 853 through 855' Processing helix chain 'E' and resid 856 through 870 removed outlier: 3.519A pdb=" N VAL E 861 " --> pdb=" O GLY E 857 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.866A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP E 944 " --> pdb=" O ARG E 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 426 removed outlier: 3.562A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 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 452 through 468 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 480 through 491 Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 528 through 540 removed outlier: 3.591A pdb=" N ILE F 532 " --> pdb=" O GLY F 528 " (cutoff:3.500A) 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 571 through 581 Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.846A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.673A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 removed outlier: 3.822A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 673 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 673 through 683 Processing helix chain 'F' and resid 692 through 704 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 738 through 747 removed outlier: 4.266A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 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 833 through 838 removed outlier: 3.508A pdb=" N THR F 837 " --> pdb=" O ASP F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 removed outlier: 3.554A pdb=" N VAL F 861 " --> pdb=" O GLY F 857 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.899A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 543 through 548 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) removed outlier: 3.746A pdb=" N LEU A 634 " --> pdb=" O PRO A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.520A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 800 through 803 removed outlier: 5.976A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N VAL A 764 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N MET A 879 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET A 766 " --> pdb=" O MET A 879 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 851 through 852 removed outlier: 3.658A pdb=" N ASP A 852 " --> pdb=" O UNK I 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA7, first strand: chain 'B' and resid 544 through 546 removed outlier: 6.220A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.710A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 799 through 803 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) removed outlier: 10.140A pdb=" N VAL B 764 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N MET B 879 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET B 766 " --> pdb=" O MET B 879 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 851 through 852 removed outlier: 3.686A pdb=" N ASP B 852 " --> pdb=" O UNK H 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB3, first strand: chain 'C' and resid 543 through 548 removed outlier: 3.561A pdb=" N LEU C 634 " --> pdb=" O PRO C 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB5, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.619A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 800 through 803 removed outlier: 5.901A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL C 764 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N MET C 879 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET C 766 " --> pdb=" O MET C 879 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB8, first strand: chain 'D' and resid 543 through 548 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) removed outlier: 7.701A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 619 through 620 Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 691 removed outlier: 7.040A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 799 through 803 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) removed outlier: 9.981A pdb=" N VAL D 764 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N MET D 879 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET D 766 " --> pdb=" O MET D 879 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA D 878 " --> pdb=" O VAL D 911 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC4, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.682A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 654 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 619 through 620 Processing sheet with id=AC6, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.153A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 800 through 803 removed outlier: 6.013A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N VAL E 764 " --> pdb=" O LEU E 877 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N MET E 879 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET E 766 " --> pdb=" O MET E 879 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AC9, first strand: chain 'F' and resid 543 through 548 removed outlier: 6.123A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) 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) Processing sheet with id=AD1, first strand: chain 'F' and resid 689 through 690 Processing sheet with id=AD2, first strand: chain 'F' and resid 800 through 803 removed outlier: 5.987A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N VAL F 764 " --> pdb=" O LEU F 877 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N MET F 879 " --> pdb=" O VAL F 764 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET F 766 " --> pdb=" O MET F 879 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 800 through 803 removed outlier: 5.987A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 882 through 883 1201 hydrogen bonds defined for protein. 3501 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: 6.21 Time building geometry restraints manager: 2.76 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: 0.00 - 2.32: 34473 2.32 - 4.64: 203 4.64 - 6.96: 27 6.96 - 9.28: 4 9.28 - 11.61: 3 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: 14618 26.82 - 53.64: 986 53.64 - 80.45: 81 80.45 - 107.27: 19 107.27 - 134.09: 2 Dihedral angle restraints: 15706 sinusoidal: 6417 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 15703 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: 100 2.42 - 3.04: 15217 3.04 - 3.66: 38484 3.66 - 4.28: 59030 4.28 - 4.90: 97567 Nonbonded interactions: 210398 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 3.040 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 3.040 ... (remaining 210393 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: 0.00 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 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: 20.720 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.000 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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= 0.091 Angle : 0.440 11.605 34710 Z= 0.222 Chirality : 0.037 0.131 3976 Planarity : 0.002 0.040 4451 Dihedral : 16.721 134.088 9716 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.88 % Allowed : 19.65 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 710 TYR 0.008 0.001 TYR D 939 PHE 0.005 0.001 PHE D 547 TRP 0.002 0.000 TRP F 770 HIS 0.002 0.000 HIS C 433 Details of bonding type rmsd covalent geometry : bond 0.00185 (25631) covalent geometry : angle 0.43963 (34710) hydrogen bonds : bond 0.22980 ( 1189) hydrogen bonds : angle 6.95977 ( 3501) *********************** 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 to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 1.040 Fit side-chains REVERT: C 773 MET cc_start: 0.8568 (mmt) cc_final: 0.7835 (mmm) outliers start: 51 outliers final: 40 residues processed: 136 average time/residue: 0.5485 time to fit residues: 88.5888 Evaluate side-chains 120 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 744 ASP Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 625 ASP Chi-restraints excluded: chain E residue 637 CYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 803 THR Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 451 HIS D 616 ASN D 805 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.032556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.026091 restraints weight = 185388.967| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.43 r_work: 0.2784 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 25631 Z= 0.234 Angle : 0.570 6.966 34710 Z= 0.293 Chirality : 0.043 0.150 3976 Planarity : 0.004 0.043 4451 Dihedral : 8.809 128.887 3685 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.88 % Allowed : 18.61 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3157 helix: 1.97 (0.13), residues: 1458 sheet: 1.56 (0.25), residues: 417 loop : -0.03 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 538 TYR 0.019 0.002 TYR B 939 PHE 0.016 0.002 PHE F 820 TRP 0.006 0.001 TRP F 770 HIS 0.006 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00550 (25631) covalent geometry : angle 0.57047 (34710) hydrogen bonds : bond 0.04690 ( 1189) hydrogen bonds : angle 5.10463 ( 3501) *********************** 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 160 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 82 time to evaluate : 1.061 Fit side-chains REVERT: B 786 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7341 (mtm180) REVERT: C 773 MET cc_start: 0.9131 (mmt) cc_final: 0.8351 (mmm) REVERT: E 846 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: F 552 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.4777 (mmt) REVERT: F 904 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8613 (ttm170) outliers start: 78 outliers final: 34 residues processed: 151 average time/residue: 0.5977 time to fit residues: 106.1731 Evaluate side-chains 118 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 846 GLU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 552 MET Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 904 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 279 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS F 805 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.045873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.033955 restraints weight = 149842.648| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.23 r_work: 0.2782 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25631 Z= 0.125 Angle : 0.489 9.257 34710 Z= 0.246 Chirality : 0.040 0.294 3976 Planarity : 0.003 0.047 4451 Dihedral : 8.422 123.405 3655 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.95 % Allowed : 18.76 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.15), residues: 3157 helix: 2.16 (0.13), residues: 1458 sheet: 1.41 (0.24), residues: 429 loop : -0.09 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 542 TYR 0.012 0.001 TYR B 939 PHE 0.014 0.001 PHE F 820 TRP 0.006 0.001 TRP F 770 HIS 0.011 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00289 (25631) covalent geometry : angle 0.48911 (34710) hydrogen bonds : bond 0.03911 ( 1189) hydrogen bonds : angle 4.81409 ( 3501) *********************** 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 161 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 81 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 786 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7286 (mtm180) REVERT: D 786 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7722 (mtm110) REVERT: E 489 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8965 (pp20) REVERT: E 846 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: F 552 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.4800 (mmt) REVERT: F 904 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8543 (ttm170) outliers start: 80 outliers final: 33 residues processed: 151 average time/residue: 0.6451 time to fit residues: 113.6624 Evaluate side-chains 119 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 846 GLU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 552 MET Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 904 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 122 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 301 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS F 713 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.033278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.026823 restraints weight = 183683.530| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.44 r_work: 0.2816 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25631 Z= 0.102 Angle : 0.477 9.815 34710 Z= 0.237 Chirality : 0.040 0.254 3976 Planarity : 0.003 0.047 4451 Dihedral : 8.146 119.140 3648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.29 % Allowed : 19.72 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.81 (0.15), residues: 3157 helix: 2.24 (0.13), residues: 1465 sheet: 1.42 (0.24), residues: 431 loop : -0.10 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.010 0.001 TYR B 939 PHE 0.012 0.001 PHE F 820 TRP 0.007 0.001 TRP E 464 HIS 0.005 0.001 HIS F 841 Details of bonding type rmsd covalent geometry : bond 0.00231 (25631) covalent geometry : angle 0.47730 (34710) hydrogen bonds : bond 0.03413 ( 1189) hydrogen bonds : angle 4.62654 ( 3501) *********************** 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 143 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 81 time to evaluate : 1.043 Fit side-chains REVERT: B 786 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7362 (mtm180) REVERT: C 773 MET cc_start: 0.9047 (mmt) cc_final: 0.8302 (mmm) REVERT: D 786 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7769 (mtm110) REVERT: E 489 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.9071 (pp20) REVERT: E 846 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8815 (mp0) REVERT: F 552 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.4740 (mmt) REVERT: F 904 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8580 (ttm170) outliers start: 62 outliers final: 29 residues processed: 137 average time/residue: 0.6747 time to fit residues: 107.3730 Evaluate side-chains 115 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 846 GLU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 552 MET Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 904 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 141 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 295 optimal weight: 0.8980 chunk 226 optimal weight: 0.3980 chunk 194 optimal weight: 8.9990 chunk 199 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 113 optimal weight: 0.0970 chunk 276 optimal weight: 0.0270 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.033734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.027274 restraints weight = 183316.748| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.45 r_work: 0.2836 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1553 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= 0.085 Angle : 0.469 9.744 34710 Z= 0.230 Chirality : 0.039 0.211 3976 Planarity : 0.003 0.047 4451 Dihedral : 7.896 114.249 3642 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.22 % Allowed : 19.98 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.15), residues: 3157 helix: 2.32 (0.14), residues: 1466 sheet: 1.39 (0.24), residues: 431 loop : -0.07 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 542 TYR 0.008 0.001 TYR A 939 PHE 0.010 0.001 PHE F 820 TRP 0.008 0.001 TRP F 770 HIS 0.023 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00183 (25631) covalent geometry : angle 0.46901 (34710) hydrogen bonds : bond 0.03112 ( 1189) hydrogen bonds : angle 4.48873 ( 3501) *********************** 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 140 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 80 time to evaluate : 0.990 Fit side-chains REVERT: C 773 MET cc_start: 0.9017 (mmt) cc_final: 0.8441 (mmm) REVERT: D 786 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7770 (mtm110) REVERT: E 846 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8843 (mp0) outliers start: 60 outliers final: 27 residues processed: 133 average time/residue: 0.6080 time to fit residues: 94.9211 Evaluate side-chains 109 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 846 GLU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 196 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 276 optimal weight: 0.0370 chunk 303 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.033559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.027097 restraints weight = 184084.036| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.45 r_work: 0.2828 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25631 Z= 0.100 Angle : 0.472 10.115 34710 Z= 0.231 Chirality : 0.039 0.149 3976 Planarity : 0.003 0.047 4451 Dihedral : 7.759 116.863 3641 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.47 % Allowed : 19.68 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.15), residues: 3157 helix: 2.35 (0.14), residues: 1466 sheet: 1.41 (0.24), residues: 421 loop : -0.08 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.011 0.001 TYR B 939 PHE 0.011 0.001 PHE F 820 TRP 0.005 0.001 TRP F 464 HIS 0.004 0.001 HIS F 841 Details of bonding type rmsd covalent geometry : bond 0.00231 (25631) covalent geometry : angle 0.47203 (34710) hydrogen bonds : bond 0.03108 ( 1189) hydrogen bonds : angle 4.42873 ( 3501) *********************** 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 150 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 83 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 805 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8002 (mp-120) REVERT: B 786 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7474 (mtm180) REVERT: C 773 MET cc_start: 0.9046 (mmt) cc_final: 0.8437 (mmm) REVERT: D 786 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7826 (mtm110) REVERT: E 846 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8854 (mp0) REVERT: F 904 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8577 (ttm170) outliers start: 67 outliers final: 35 residues processed: 143 average time/residue: 0.6439 time to fit residues: 107.2289 Evaluate side-chains 121 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 846 GLU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 904 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 97 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 chunk 316 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS B 515 GLN B 618 ASN F 805 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.031868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.025448 restraints weight = 186480.050| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.41 r_work: 0.2751 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 25631 Z= 0.291 Angle : 0.621 11.368 34710 Z= 0.313 Chirality : 0.044 0.185 3976 Planarity : 0.005 0.046 4451 Dihedral : 8.197 128.250 3641 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.62 % Allowed : 19.72 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3157 helix: 1.97 (0.13), residues: 1452 sheet: 1.07 (0.25), residues: 417 loop : -0.28 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 940 TYR 0.023 0.002 TYR B 939 PHE 0.022 0.002 PHE F 820 TRP 0.007 0.001 TRP F 770 HIS 0.007 0.001 HIS C 843 Details of bonding type rmsd covalent geometry : bond 0.00692 (25631) covalent geometry : angle 0.62076 (34710) hydrogen bonds : bond 0.04253 ( 1189) hydrogen bonds : angle 4.83515 ( 3501) *********************** 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 to be fit. rotamer outliers: 71 poor density : 80 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 786 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7405 (mtm180) REVERT: C 773 MET cc_start: 0.9127 (mmt) cc_final: 0.8380 (mmm) REVERT: D 786 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7875 (mtm110) REVERT: E 846 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: F 904 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8618 (ttm170) outliers start: 71 outliers final: 35 residues processed: 141 average time/residue: 0.6700 time to fit residues: 110.0901 Evaluate side-chains 118 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 846 GLU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 904 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 283 optimal weight: 0.5980 chunk 271 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS B 618 ASN F 622 HIS F 713 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.031894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025482 restraints weight = 186134.505| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.41 r_work: 0.2754 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 25631 Z= 0.251 Angle : 0.594 14.240 34710 Z= 0.296 Chirality : 0.043 0.247 3976 Planarity : 0.004 0.050 4451 Dihedral : 8.166 130.147 3641 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.51 % Allowed : 19.98 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3157 helix: 1.87 (0.13), residues: 1452 sheet: 0.91 (0.25), residues: 419 loop : -0.41 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 940 TYR 0.020 0.002 TYR B 939 PHE 0.017 0.002 PHE F 820 TRP 0.006 0.001 TRP F 770 HIS 0.007 0.001 HIS C 843 Details of bonding type rmsd covalent geometry : bond 0.00594 (25631) covalent geometry : angle 0.59360 (34710) hydrogen bonds : bond 0.03956 ( 1189) hydrogen bonds : angle 4.81561 ( 3501) *********************** 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 148 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 80 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: B 786 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7386 (mtm180) REVERT: C 773 MET cc_start: 0.9115 (mmt) cc_final: 0.8519 (mmm) REVERT: D 786 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7871 (mtm110) REVERT: F 904 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8624 (ttm170) outliers start: 68 outliers final: 41 residues processed: 140 average time/residue: 0.6255 time to fit residues: 102.8424 Evaluate side-chains 123 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 79 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 904 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 154 optimal weight: 0.5980 chunk 254 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS B 618 ASN ** F 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.032693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026268 restraints weight = 184797.322| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.44 r_work: 0.2794 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25631 Z= 0.113 Angle : 0.527 13.056 34710 Z= 0.257 Chirality : 0.040 0.317 3976 Planarity : 0.003 0.050 4451 Dihedral : 7.867 127.850 3640 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 20.75 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3157 helix: 2.14 (0.13), residues: 1459 sheet: 0.97 (0.24), residues: 431 loop : -0.30 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 542 TYR 0.012 0.001 TYR B 939 PHE 0.013 0.001 PHE F 820 TRP 0.007 0.001 TRP F 770 HIS 0.004 0.001 HIS F 841 Details of bonding type rmsd covalent geometry : bond 0.00261 (25631) covalent geometry : angle 0.52686 (34710) hydrogen bonds : bond 0.03288 ( 1189) hydrogen bonds : angle 4.61331 ( 3501) *********************** 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 127 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: B 786 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7464 (mtm180) REVERT: C 773 MET cc_start: 0.9072 (mmt) cc_final: 0.8445 (mmm) REVERT: D 786 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7825 (mtm110) outliers start: 46 outliers final: 32 residues processed: 124 average time/residue: 0.6754 time to fit residues: 97.5659 Evaluate side-chains 115 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 62 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 20 optimal weight: 0.0170 chunk 294 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS B 618 ASN F 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.032775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.026343 restraints weight = 184879.552| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.44 r_work: 0.2797 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25631 Z= 0.116 Angle : 0.532 14.629 34710 Z= 0.257 Chirality : 0.040 0.318 3976 Planarity : 0.003 0.050 4451 Dihedral : 7.784 127.178 3640 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.59 % Allowed : 21.05 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.15), residues: 3157 helix: 2.19 (0.13), residues: 1459 sheet: 0.96 (0.24), residues: 431 loop : -0.26 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 542 TYR 0.012 0.001 TYR B 939 PHE 0.013 0.001 PHE F 820 TRP 0.005 0.001 TRP F 770 HIS 0.004 0.001 HIS F 841 Details of bonding type rmsd covalent geometry : bond 0.00270 (25631) covalent geometry : angle 0.53156 (34710) hydrogen bonds : bond 0.03254 ( 1189) hydrogen bonds : angle 4.58365 ( 3501) ********************** 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 123 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 552 MET cc_start: 0.8858 (ttp) cc_final: 0.8610 (tmt) REVERT: B 786 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7476 (mtm180) REVERT: C 773 MET cc_start: 0.9057 (mmt) cc_final: 0.8429 (mmm) REVERT: D 786 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7815 (mtm110) outliers start: 43 outliers final: 31 residues processed: 120 average time/residue: 0.6594 time to fit residues: 92.3441 Evaluate side-chains 113 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 626 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 95 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 283 optimal weight: 1.9990 chunk 307 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 451 HIS B 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.033466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027033 restraints weight = 183257.733| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.44 r_work: 0.2827 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25631 Z= 0.093 Angle : 0.510 13.026 34710 Z= 0.245 Chirality : 0.040 0.301 3976 Planarity : 0.003 0.051 4451 Dihedral : 7.509 124.023 3640 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.26 % Allowed : 21.49 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.15), residues: 3157 helix: 2.27 (0.14), residues: 1469 sheet: 1.03 (0.24), residues: 419 loop : -0.18 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 652 TYR 0.008 0.001 TYR A 939 PHE 0.011 0.001 PHE D 547 TRP 0.009 0.001 TRP F 770 HIS 0.003 0.001 HIS F 841 Details of bonding type rmsd covalent geometry : bond 0.00211 (25631) covalent geometry : angle 0.51046 (34710) hydrogen bonds : bond 0.02922 ( 1189) hydrogen bonds : angle 4.44055 ( 3501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7818.62 seconds wall clock time: 134 minutes 26.21 seconds (8066.21 seconds total)