Starting phenix.real_space_refine on Thu Jan 15 10:34:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p09_13146/01_2026/7p09_13146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p09_13146/01_2026/7p09_13146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p09_13146/01_2026/7p09_13146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p09_13146/01_2026/7p09_13146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p09_13146/01_2026/7p09_13146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p09_13146/01_2026/7p09_13146.map" } resolution = 2.7 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= 0.045 sd= 0.684 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 15856 2.51 5 N 4294 2.21 5 O 4801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s 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: 25091 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4164 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Chain: "B" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4186 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 510} Chain breaks: 1 Chain: "C" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4152 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 506} Chain breaks: 1 Chain: "D" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4145 Classifications: {'peptide': 531} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 506} Chain breaks: 1 Chain: "E" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4148 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 506} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 4059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4059 Classifications: {'peptide': 520} Modifications used: {'COO': 1} 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: "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: 6.41, per 1000 atoms: 0.26 Number of scatterers: 25091 At special positions: 0 Unit cell: (131.454, 135.378, 139.956, 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 4801 8.00 N 4294 7.00 C 15856 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: 2.08 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: 5942 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 28 sheets defined 53.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.500A pdb=" N ARG A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.837A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 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: 3.711A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 535 " --> pdb=" O SER A 531 " (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 591 through 595 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.760A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.901A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.841A 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 703 Processing helix chain 'A' and resid 711 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: 3.892A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 removed outlier: 3.595A pdb=" N GLN A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 removed outlier: 3.535A pdb=" N THR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' 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: 3.952A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 944 " --> pdb=" O ARG A 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.646A pdb=" N ASN B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.763A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.984A pdb=" N ALA B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (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 605 through 611 removed outlier: 4.345A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.996A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 652 removed outlier: 3.631A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 removed outlier: 3.680A pdb=" N ALA B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.588A pdb=" N GLN B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) 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: 3.804A 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 removed outlier: 3.529A pdb=" N THR B 837 " --> pdb=" O ASP B 833 " (cutoff:3.500A) 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: 3.885A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 944 " --> pdb=" O ARG B 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 removed outlier: 3.717A pdb=" N ARG C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.767A pdb=" N ASN C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 4.281A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 3.736A 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: 3.793A pdb=" N ALA C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.542A 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 591 through 595 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.815A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.548A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.704A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.866A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 738 through 747 removed outlier: 4.195A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 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: 3.878A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 removed outlier: 3.634A pdb=" N PHE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 425 " --> pdb=" O PHE D 421 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 452 through 467 removed outlier: 3.943A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 457 " --> pdb=" O SER D 453 " (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 528 through 541 removed outlier: 3.533A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (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: 4.046A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 4.133A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.538A 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: 3.840A pdb=" N CYS D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.590A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.000A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 425 removed outlier: 3.533A pdb=" N PHE E 421 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.646A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 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: 3.818A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 removed outlier: 3.732A pdb=" N LYS E 559 " --> pdb=" O VAL E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'E' and resid 603 through 612 removed outlier: 3.550A pdb=" N LEU E 607 " --> pdb=" O PRO E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 618 removed outlier: 4.408A pdb=" N ASN E 618 " --> pdb=" O GLU E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 645 removed outlier: 3.961A pdb=" N THR E 644 " --> pdb=" O VAL E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 652 removed outlier: 4.133A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 682 Processing helix chain 'E' and resid 692 through 704 removed outlier: 3.664A pdb=" N CYS E 704 " --> pdb=" O ILE E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 741 through 747 removed outlier: 3.992A pdb=" N PHE E 745 " --> pdb=" O ASN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 833 through 838 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 Processing helix chain 'E' and resid 894 through 906 removed outlier: 3.526A pdb=" N ILE E 900 " --> pdb=" O LYS E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.921A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 426 removed outlier: 3.505A pdb=" N GLU F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.852A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.621A pdb=" N VAL F 457 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG F 459 " --> pdb=" O PHE F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 491 removed outlier: 3.591A pdb=" N GLN F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA F 485 " --> pdb=" O ALA F 481 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 528 through 540 removed outlier: 3.780A pdb=" N ALA F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.622A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 618 removed outlier: 3.661A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN F 618 " --> pdb=" O GLU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 removed outlier: 3.905A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 673 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 741 through 746 Processing helix chain 'F' and resid 807 through 829 removed outlier: 3.665A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 827 " --> pdb=" O ALA F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 833 through 838 removed outlier: 3.615A 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 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: 3.906A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 7.040A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.625A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.108A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.749A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA6, first strand: chain 'B' and resid 543 through 548 removed outlier: 6.454A pdb=" N GLU B 543 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 588 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.627A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 800 through 802 removed outlier: 6.190A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N VAL B 764 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N MET B 879 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 766 " --> pdb=" O MET B 879 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB1, first strand: chain 'C' and resid 543 through 548 removed outlier: 6.844A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.628A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 764 through 769 Processing sheet with id=AB4, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.908A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB6, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.722A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.718A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 799 through 803 removed outlier: 6.312A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N VAL D 764 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N MET D 879 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET D 766 " --> pdb=" O MET D 879 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA D 878 " --> pdb=" O VAL D 911 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC1, first strand: chain 'E' and resid 543 through 548 removed outlier: 6.147A pdb=" N GLU E 543 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU E 588 " --> pdb=" O GLU E 543 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE E 636 " --> pdb=" O PRO E 585 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.294A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 764 through 769 removed outlier: 6.125A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.757A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AC6, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.442A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 689 through 690 Processing sheet with id=AC8, first strand: chain 'F' and resid 799 through 803 removed outlier: 6.182A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N VAL F 764 " --> pdb=" O LEU F 877 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N MET F 879 " --> pdb=" O VAL F 764 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET F 766 " --> pdb=" O MET F 879 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 910 " --> pdb=" O GLU F 932 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 769 through 771 Processing sheet with id=AD1, first strand: chain 'F' and resid 882 through 883 removed outlier: 3.540A pdb=" N GLU F 882 " --> pdb=" O LEU F 890 " (cutoff:3.500A) 1167 hydrogen bonds defined for protein. 3411 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: 4.72 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4282 1.30 - 1.43: 5981 1.43 - 1.56: 15054 1.56 - 1.68: 28 1.68 - 1.81: 198 Bond restraints: 25543 Sorted by residual: bond pdb=" C PRO B 524 " pdb=" O PRO B 524 " ideal model delta sigma weight residual 1.240 1.177 0.063 1.12e-02 7.97e+03 3.19e+01 bond pdb=" CA SER B 531 " pdb=" CB SER B 531 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.59e-02 3.96e+03 2.09e+01 bond pdb=" CA SER A 531 " pdb=" CB SER A 531 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.56e-02 4.11e+03 1.86e+01 bond pdb=" CA ALA B 668 " pdb=" CB ALA B 668 " ideal model delta sigma weight residual 1.534 1.462 0.071 1.71e-02 3.42e+03 1.74e+01 bond pdb=" CA ALA B 670 " pdb=" CB ALA B 670 " ideal model delta sigma weight residual 1.532 1.464 0.067 1.62e-02 3.81e+03 1.73e+01 ... (remaining 25538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 33935 1.60 - 3.21: 510 3.21 - 4.81: 114 4.81 - 6.42: 29 6.42 - 8.02: 4 Bond angle restraints: 34592 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 131.85 8.02 1.00e+00 1.00e+00 6.43e+01 angle pdb=" PB ATP B1001 " pdb=" O3B ATP B1001 " pdb=" PG ATP B1001 " ideal model delta sigma weight residual 139.87 132.09 7.78 1.00e+00 1.00e+00 6.05e+01 angle pdb=" N ASN A 711 " pdb=" CA ASN A 711 " pdb=" C ASN A 711 " ideal model delta sigma weight residual 113.41 105.78 7.63 1.22e+00 6.72e-01 3.91e+01 angle pdb=" PA ATP B1001 " pdb=" O3A ATP B1001 " pdb=" PB ATP B1001 " ideal model delta sigma weight residual 136.83 130.73 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" N ILE B 669 " pdb=" CA ILE B 669 " pdb=" C ILE B 669 " ideal model delta sigma weight residual 113.07 105.71 7.36 1.37e+00 5.33e-01 2.88e+01 ... (remaining 34587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.23: 14933 26.23 - 52.45: 663 52.45 - 78.68: 53 78.68 - 104.90: 14 104.90 - 131.13: 3 Dihedral angle restraints: 15666 sinusoidal: 6443 harmonic: 9223 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 300.00 168.87 131.13 1 2.00e+01 2.50e-03 3.98e+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 50.76 -110.77 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" O2A ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PA ADP D1001 " pdb=" PB ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 45.95 -105.95 1 2.00e+01 2.50e-03 3.06e+01 ... (remaining 15663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3470 0.061 - 0.123: 438 0.123 - 0.184: 32 0.184 - 0.246: 8 0.246 - 0.307: 4 Chirality restraints: 3952 Sorted by residual: chirality pdb=" CA SER B 531 " pdb=" N SER B 531 " pdb=" C SER B 531 " pdb=" CB SER B 531 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ARG B 710 " pdb=" N ARG B 710 " pdb=" C ARG B 710 " pdb=" CB ARG B 710 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA TYR B 492 " pdb=" N TYR B 492 " pdb=" C TYR B 492 " pdb=" CB TYR B 492 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3949 not shown) Planarity restraints: 4439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 667 " -0.018 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C LEU B 667 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU B 667 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA B 668 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 528 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C GLY A 528 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY A 528 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 529 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 669 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C ILE B 669 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 669 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 670 " 0.012 2.00e-02 2.50e+03 ... (remaining 4436 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 95 2.45 - 3.06: 16048 3.06 - 3.68: 38130 3.68 - 4.29: 58211 4.29 - 4.90: 95007 Nonbonded interactions: 207491 Sorted by model distance: nonbonded pdb=" O2G ATP C1001 " pdb="MG MG C1002 " model vdw 1.839 2.170 nonbonded pdb=" O2G ATP B1001 " pdb="MG MG B1002 " model vdw 1.855 2.170 nonbonded pdb=" O2G ATP A1001 " pdb="MG MG A1002 " model vdw 1.899 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1002 " model vdw 1.902 2.170 nonbonded pdb=" OG1 THR A 530 " pdb="MG MG A1002 " model vdw 1.926 2.170 ... (remaining 207486 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 571 or (resid 572 and \ (name N or name CA or name C or name O or name CB )) or resid 573 through 594 o \ r resid 602 through 786 or resid 796 through 949)) selection = (chain 'B' and (resid 410 through 562 or resid 568 through 571 or (resid 572 and \ (name N or name CA or name C or name O or name CB )) or resid 573 through 594 o \ r resid 602 through 786 or resid 790 through 795 or resid 798 through 949)) selection = (chain 'C' and (resid 410 through 562 or resid 568 through 571 or (resid 572 and \ (name N or name CA or name C or name O or name CB )) or resid 573 through 594 o \ r resid 602 through 786 or resid 796 through 949)) selection = (chain 'D' and (resid 410 through 562 or resid 568 through 571 or (resid 572 and \ (name N or name CA or name C or name O or name CB )) or resid 573 through 594 o \ r resid 602 through 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 571 or (resid 572 and (name N or name CA or na \ me C or name O or name CB )) or resid 573 through 786 or resid 796 through 949)) \ } 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: 15.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.940 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25543 Z= 0.189 Angle : 0.521 8.020 34592 Z= 0.299 Chirality : 0.042 0.307 3952 Planarity : 0.003 0.066 4439 Dihedral : 13.852 131.127 9724 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3157 helix: 1.08 (0.13), residues: 1410 sheet: 0.75 (0.26), residues: 408 loop : -0.07 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 652 TYR 0.014 0.001 TYR B 673 PHE 0.019 0.001 PHE E 547 TRP 0.018 0.001 TRP F 470 HIS 0.006 0.001 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00309 (25543) covalent geometry : angle 0.52137 (34592) hydrogen bonds : bond 0.24397 ( 1167) hydrogen bonds : angle 7.38231 ( 3411) *********************** 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 392 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.955 Fit side-chains REVERT: A 518 ILE cc_start: 0.7969 (mm) cc_final: 0.7693 (mm) REVERT: D 638 THR cc_start: 0.8645 (m) cc_final: 0.8354 (m) REVERT: D 766 MET cc_start: 0.8116 (ttt) cc_final: 0.7716 (ttp) REVERT: E 636 ILE cc_start: 0.8066 (mm) cc_final: 0.7827 (mm) outliers start: 0 outliers final: 1 residues processed: 392 average time/residue: 0.7652 time to fit residues: 339.5360 Evaluate side-chains 239 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 573 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS B 450 ASN B 618 ASN B 640 ASN B 827 GLN C 615 GLN C 622 HIS C 702 GLN D 934 HIS F 484 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092699 restraints weight = 38410.193| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.35 r_work: 0.3107 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25543 Z= 0.257 Angle : 0.631 8.526 34592 Z= 0.325 Chirality : 0.045 0.193 3952 Planarity : 0.005 0.047 4439 Dihedral : 8.579 116.718 3619 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 9.55 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3157 helix: 1.30 (0.13), residues: 1469 sheet: 0.67 (0.25), residues: 413 loop : -0.47 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 563 TYR 0.023 0.002 TYR F 623 PHE 0.020 0.002 PHE B 820 TRP 0.008 0.001 TRP F 470 HIS 0.006 0.001 HIS C 622 Details of bonding type rmsd covalent geometry : bond 0.00608 (25543) covalent geometry : angle 0.63148 (34592) hydrogen bonds : bond 0.04850 ( 1167) hydrogen bonds : angle 5.18660 ( 3411) *********************** 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 322 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7026 (mtmm) REVERT: A 569 MET cc_start: 0.8279 (mtm) cc_final: 0.8012 (mtm) REVERT: A 655 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7268 (mpt) REVERT: B 733 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: C 419 GLU cc_start: 0.8008 (tp30) cc_final: 0.7672 (pm20) REVERT: C 432 LYS cc_start: 0.7704 (tppt) cc_final: 0.7256 (tptm) REVERT: C 435 MET cc_start: 0.8819 (mmm) cc_final: 0.8618 (mmm) REVERT: D 489 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7759 (tm-30) REVERT: D 609 GLU cc_start: 0.8471 (tt0) cc_final: 0.7692 (tm-30) REVERT: D 766 MET cc_start: 0.8931 (ttt) cc_final: 0.8593 (ttm) REVERT: D 922 ASP cc_start: 0.8270 (t0) cc_final: 0.8058 (t0) REVERT: E 496 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7279 (p0) REVERT: E 588 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8123 (tt) REVERT: F 581 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7447 (mmtt) REVERT: F 897 GLU cc_start: 0.8465 (mp0) cc_final: 0.8142 (mp0) outliers start: 58 outliers final: 18 residues processed: 297 average time/residue: 0.7215 time to fit residues: 245.1835 Evaluate side-chains 250 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 776 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 240 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 219 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 827 GLN C 477 ASN D 664 GLN F 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.127069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095790 restraints weight = 38188.476| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.29 r_work: 0.3146 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25543 Z= 0.124 Angle : 0.515 7.764 34592 Z= 0.263 Chirality : 0.041 0.150 3952 Planarity : 0.004 0.036 4439 Dihedral : 8.320 115.319 3617 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.70 % Allowed : 12.86 % Favored : 85.44 % 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: 1.01 (0.15), residues: 3157 helix: 1.64 (0.13), residues: 1477 sheet: 0.63 (0.25), residues: 413 loop : -0.43 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 652 TYR 0.020 0.001 TYR F 623 PHE 0.016 0.001 PHE A 547 TRP 0.008 0.001 TRP F 470 HIS 0.004 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00285 (25543) covalent geometry : angle 0.51538 (34592) hydrogen bonds : bond 0.04009 ( 1167) hydrogen bonds : angle 4.83085 ( 3411) *********************** 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 310 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7586 (ttpt) REVERT: A 441 GLU cc_start: 0.7821 (tp30) cc_final: 0.7114 (tp30) REVERT: A 569 MET cc_start: 0.8234 (mtm) cc_final: 0.7839 (mtm) REVERT: B 949 ASP cc_start: 0.7613 (m-30) cc_final: 0.6114 (p0) REVERT: C 475 ASN cc_start: 0.8525 (t0) cc_final: 0.7484 (p0) REVERT: C 647 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7767 (tm-30) REVERT: D 609 GLU cc_start: 0.8454 (tt0) cc_final: 0.7679 (tm-30) REVERT: D 766 MET cc_start: 0.8696 (ttt) cc_final: 0.8345 (ttp) REVERT: D 846 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6387 (tm-30) REVERT: E 588 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8141 (tt) REVERT: E 686 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7435 (pp20) REVERT: F 496 ASP cc_start: 0.8497 (m-30) cc_final: 0.8254 (m-30) REVERT: F 581 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7464 (tppt) REVERT: F 897 GLU cc_start: 0.8435 (mp0) cc_final: 0.8038 (mp0) outliers start: 46 outliers final: 9 residues processed: 291 average time/residue: 0.7221 time to fit residues: 240.7265 Evaluate side-chains 244 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 686 GLU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 655 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 30 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 227 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 314 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 477 ASN D 664 GLN F 713 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094180 restraints weight = 38167.584| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.28 r_work: 0.3127 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25543 Z= 0.167 Angle : 0.544 9.754 34592 Z= 0.275 Chirality : 0.042 0.157 3952 Planarity : 0.004 0.039 4439 Dihedral : 8.239 122.504 3617 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.99 % Allowed : 14.26 % Favored : 83.74 % 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: 1.01 (0.15), residues: 3157 helix: 1.66 (0.13), residues: 1479 sheet: 0.63 (0.25), residues: 411 loop : -0.47 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 652 TYR 0.021 0.001 TYR F 623 PHE 0.026 0.001 PHE A 547 TRP 0.006 0.001 TRP F 470 HIS 0.004 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00394 (25543) covalent geometry : angle 0.54359 (34592) hydrogen bonds : bond 0.03876 ( 1167) hydrogen bonds : angle 4.72880 ( 3411) *********************** 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 295 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7559 (ttpt) REVERT: A 441 GLU cc_start: 0.7882 (tp30) cc_final: 0.7118 (tp30) REVERT: A 569 MET cc_start: 0.8240 (mtm) cc_final: 0.7886 (mtm) REVERT: A 576 CYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 432 LYS cc_start: 0.8495 (tppt) cc_final: 0.8250 (tptp) REVERT: B 460 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8189 (t0) REVERT: B 717 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: B 949 ASP cc_start: 0.7660 (m-30) cc_final: 0.6131 (p0) REVERT: C 475 ASN cc_start: 0.8513 (t0) cc_final: 0.7536 (p0) REVERT: C 643 ASP cc_start: 0.8222 (m-30) cc_final: 0.7757 (p0) REVERT: C 647 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7851 (tp30) REVERT: D 609 GLU cc_start: 0.8446 (tt0) cc_final: 0.7660 (tm-30) REVERT: D 766 MET cc_start: 0.8852 (ttt) cc_final: 0.8531 (ttm) REVERT: D 846 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6546 (tm-30) REVERT: E 588 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8125 (tt) REVERT: F 496 ASP cc_start: 0.8498 (m-30) cc_final: 0.8253 (m-30) REVERT: F 547 PHE cc_start: 0.7102 (t80) cc_final: 0.6812 (t80) REVERT: F 581 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7495 (tppt) REVERT: F 589 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7437 (pp) REVERT: F 897 GLU cc_start: 0.8479 (mp0) cc_final: 0.8084 (mp0) outliers start: 54 outliers final: 21 residues processed: 273 average time/residue: 0.7167 time to fit residues: 224.0082 Evaluate side-chains 248 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 589 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 164 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 711 ASN F 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095217 restraints weight = 37924.187| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3137 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25543 Z= 0.127 Angle : 0.518 7.648 34592 Z= 0.261 Chirality : 0.041 0.274 3952 Planarity : 0.004 0.038 4439 Dihedral : 8.102 125.905 3617 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.88 % Allowed : 15.44 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3157 helix: 1.78 (0.13), residues: 1480 sheet: 0.67 (0.25), residues: 411 loop : -0.43 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 652 TYR 0.022 0.001 TYR F 623 PHE 0.022 0.001 PHE A 547 TRP 0.007 0.001 TRP F 470 HIS 0.003 0.001 HIS C 843 Details of bonding type rmsd covalent geometry : bond 0.00295 (25543) covalent geometry : angle 0.51817 (34592) hydrogen bonds : bond 0.03514 ( 1167) hydrogen bonds : angle 4.62482 ( 3411) *********************** 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 301 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7536 (ttpt) REVERT: A 432 LYS cc_start: 0.7806 (tptp) cc_final: 0.7552 (tptp) REVERT: A 488 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 569 MET cc_start: 0.8209 (mtm) cc_final: 0.7793 (mtm) REVERT: A 576 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8511 (p) REVERT: B 432 LYS cc_start: 0.8482 (tppt) cc_final: 0.8264 (tptp) REVERT: B 460 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8085 (t0) REVERT: B 949 ASP cc_start: 0.7648 (m-30) cc_final: 0.6080 (p0) REVERT: C 475 ASN cc_start: 0.8518 (t0) cc_final: 0.7523 (p0) REVERT: C 591 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7829 (mm-30) REVERT: C 643 ASP cc_start: 0.8190 (m-30) cc_final: 0.7872 (p0) REVERT: C 647 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7823 (tp30) REVERT: C 826 MET cc_start: 0.8663 (tpp) cc_final: 0.8418 (tpt) REVERT: D 423 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: D 445 LEU cc_start: 0.6764 (mt) cc_final: 0.6551 (mp) REVERT: D 545 PHE cc_start: 0.8650 (t80) cc_final: 0.8442 (t80) REVERT: D 609 GLU cc_start: 0.8437 (tt0) cc_final: 0.7668 (tm-30) REVERT: D 766 MET cc_start: 0.8738 (ttt) cc_final: 0.8435 (ttp) REVERT: D 846 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6517 (tm-30) REVERT: E 588 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8112 (tt) REVERT: E 686 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7435 (pp20) REVERT: F 496 ASP cc_start: 0.8495 (m-30) cc_final: 0.8266 (m-30) REVERT: F 581 LYS cc_start: 0.7868 (mmtp) cc_final: 0.7506 (tppt) REVERT: F 589 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7431 (pp) REVERT: F 897 GLU cc_start: 0.8481 (mp0) cc_final: 0.8095 (mp0) outliers start: 51 outliers final: 19 residues processed: 282 average time/residue: 0.6918 time to fit residues: 224.1967 Evaluate side-chains 253 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 303 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN D 477 ASN E 711 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 = 0.3687 r_free = 0.3687 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093545 restraints weight = 38545.093| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.34 r_work: 0.3101 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25543 Z= 0.181 Angle : 0.553 9.017 34592 Z= 0.278 Chirality : 0.042 0.241 3952 Planarity : 0.004 0.038 4439 Dihedral : 8.113 133.171 3617 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.51 % Allowed : 15.44 % Favored : 82.05 % 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: 1.07 (0.15), residues: 3157 helix: 1.75 (0.13), residues: 1472 sheet: 0.61 (0.25), residues: 413 loop : -0.46 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 652 TYR 0.022 0.002 TYR F 623 PHE 0.026 0.001 PHE A 547 TRP 0.006 0.001 TRP E 464 HIS 0.007 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00430 (25543) covalent geometry : angle 0.55255 (34592) hydrogen bonds : bond 0.03819 ( 1167) hydrogen bonds : angle 4.65988 ( 3411) *********************** 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 307 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7576 (ttpt) REVERT: A 488 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 569 MET cc_start: 0.8263 (mtm) cc_final: 0.7847 (mtm) REVERT: B 460 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8050 (t0) REVERT: C 475 ASN cc_start: 0.8535 (t0) cc_final: 0.7572 (p0) REVERT: C 591 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: C 643 ASP cc_start: 0.8128 (m-30) cc_final: 0.7837 (p0) REVERT: C 647 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7870 (tp30) REVERT: D 423 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: D 445 LEU cc_start: 0.6660 (mt) cc_final: 0.6460 (mp) REVERT: D 545 PHE cc_start: 0.8652 (t80) cc_final: 0.8449 (t80) REVERT: D 609 GLU cc_start: 0.8447 (tt0) cc_final: 0.7652 (tm-30) REVERT: D 766 MET cc_start: 0.8852 (ttt) cc_final: 0.8531 (ttm) REVERT: D 846 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6462 (tm-30) REVERT: E 588 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8089 (tt) REVERT: F 547 PHE cc_start: 0.6884 (t80) cc_final: 0.6675 (t80) REVERT: F 569 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5668 (pmm) REVERT: F 581 LYS cc_start: 0.7815 (mmtp) cc_final: 0.7430 (tppt) REVERT: F 589 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7331 (pp) REVERT: F 897 GLU cc_start: 0.8496 (mp0) cc_final: 0.8097 (mp0) outliers start: 68 outliers final: 36 residues processed: 284 average time/residue: 0.6847 time to fit residues: 223.6976 Evaluate side-chains 266 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 569 MET Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 204 optimal weight: 0.0770 chunk 224 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 477 ASN E 711 ASN F 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094631 restraints weight = 38173.810| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.33 r_work: 0.3146 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25543 Z= 0.115 Angle : 0.520 8.819 34592 Z= 0.260 Chirality : 0.040 0.250 3952 Planarity : 0.004 0.039 4439 Dihedral : 7.879 132.090 3617 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.95 % Allowed : 16.88 % Favored : 81.16 % 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: 1.22 (0.15), residues: 3157 helix: 1.88 (0.13), residues: 1484 sheet: 0.69 (0.25), residues: 409 loop : -0.41 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 459 TYR 0.022 0.001 TYR F 623 PHE 0.022 0.001 PHE A 547 TRP 0.007 0.001 TRP F 470 HIS 0.005 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00265 (25543) covalent geometry : angle 0.52013 (34592) hydrogen bonds : bond 0.03297 ( 1167) hydrogen bonds : angle 4.54243 ( 3411) *********************** 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 295 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7568 (ttpt) REVERT: A 432 LYS cc_start: 0.7775 (tptp) cc_final: 0.7565 (tptp) REVERT: A 488 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 576 CYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 432 LYS cc_start: 0.8524 (tppt) cc_final: 0.8253 (tptp) REVERT: B 460 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8074 (t0) REVERT: B 618 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7549 (p0) REVERT: B 949 ASP cc_start: 0.7394 (m-30) cc_final: 0.6088 (p0) REVERT: C 475 ASN cc_start: 0.8522 (t0) cc_final: 0.7564 (p0) REVERT: C 591 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: C 643 ASP cc_start: 0.8119 (m-30) cc_final: 0.7848 (p0) REVERT: C 647 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7863 (tp30) REVERT: C 826 MET cc_start: 0.8674 (tpp) cc_final: 0.8422 (tpt) REVERT: C 896 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8775 (tttp) REVERT: D 423 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: D 477 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7422 (t0) REVERT: D 482 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7617 (ttt180) REVERT: D 488 GLU cc_start: 0.7564 (tp30) cc_final: 0.7228 (tp30) REVERT: D 609 GLU cc_start: 0.8420 (tt0) cc_final: 0.7683 (tm-30) REVERT: D 766 MET cc_start: 0.8689 (ttt) cc_final: 0.8410 (ttp) REVERT: D 846 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6429 (tm-30) REVERT: E 588 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8121 (tt) REVERT: E 591 GLU cc_start: 0.7556 (pt0) cc_final: 0.7037 (pp20) REVERT: F 581 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7506 (tppt) REVERT: F 589 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7347 (pp) REVERT: F 897 GLU cc_start: 0.8470 (mp0) cc_final: 0.8097 (mp0) outliers start: 53 outliers final: 19 residues processed: 275 average time/residue: 0.6888 time to fit residues: 217.8917 Evaluate side-chains 261 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 896 LYS Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 261 optimal weight: 0.6980 chunk 294 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 711 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094259 restraints weight = 38224.901| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.32 r_work: 0.3140 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25543 Z= 0.129 Angle : 0.531 9.606 34592 Z= 0.264 Chirality : 0.041 0.281 3952 Planarity : 0.004 0.039 4439 Dihedral : 7.832 133.246 3617 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.03 % Allowed : 17.25 % Favored : 80.72 % 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: 1.90 (0.13), residues: 1483 sheet: 0.65 (0.25), residues: 411 loop : -0.40 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.023 0.001 TYR F 623 PHE 0.022 0.001 PHE A 547 TRP 0.006 0.001 TRP F 470 HIS 0.005 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00302 (25543) covalent geometry : angle 0.53134 (34592) hydrogen bonds : bond 0.03359 ( 1167) hydrogen bonds : angle 4.53186 ( 3411) *********************** 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 292 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7569 (ttpt) REVERT: A 432 LYS cc_start: 0.7791 (tptp) cc_final: 0.7563 (tptp) REVERT: A 488 GLU cc_start: 0.8211 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 576 CYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 432 LYS cc_start: 0.8516 (tppt) cc_final: 0.8259 (tptp) REVERT: B 460 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 618 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7573 (p0) REVERT: B 949 ASP cc_start: 0.7394 (m-30) cc_final: 0.6116 (p0) REVERT: C 475 ASN cc_start: 0.8519 (t0) cc_final: 0.7567 (p0) REVERT: C 591 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: C 643 ASP cc_start: 0.8107 (m-30) cc_final: 0.7843 (p0) REVERT: C 647 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7871 (tp30) REVERT: C 826 MET cc_start: 0.8691 (tpp) cc_final: 0.8444 (tpt) REVERT: C 896 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8759 (tttp) REVERT: D 423 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: D 482 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7796 (ttm110) REVERT: D 488 GLU cc_start: 0.7583 (tp30) cc_final: 0.7260 (tp30) REVERT: D 609 GLU cc_start: 0.8428 (tt0) cc_final: 0.7679 (tm-30) REVERT: D 766 MET cc_start: 0.8738 (ttt) cc_final: 0.8467 (ttp) REVERT: D 846 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6392 (tm-30) REVERT: E 588 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8144 (tt) REVERT: E 591 GLU cc_start: 0.7698 (pt0) cc_final: 0.7029 (pp20) REVERT: F 581 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7513 (tppt) REVERT: F 589 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7356 (pp) REVERT: F 665 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: F 897 GLU cc_start: 0.8487 (mp0) cc_final: 0.8109 (mp0) REVERT: F 922 ASP cc_start: 0.8408 (t0) cc_final: 0.8165 (t0) outliers start: 55 outliers final: 33 residues processed: 272 average time/residue: 0.6784 time to fit residues: 212.4981 Evaluate side-chains 267 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 LYS Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 686 GLU Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 289 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 0.0870 chunk 232 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 308 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN F 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094573 restraints weight = 38271.424| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.31 r_work: 0.3154 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25543 Z= 0.113 Angle : 0.527 9.777 34592 Z= 0.260 Chirality : 0.041 0.307 3952 Planarity : 0.004 0.042 4439 Dihedral : 7.728 132.707 3617 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.81 % Allowed : 17.25 % Favored : 80.94 % 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: 1.29 (0.15), residues: 3157 helix: 1.96 (0.13), residues: 1485 sheet: 0.65 (0.25), residues: 411 loop : -0.38 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.024 0.001 TYR F 623 PHE 0.021 0.001 PHE A 547 TRP 0.006 0.001 TRP F 770 HIS 0.005 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00263 (25543) covalent geometry : angle 0.52662 (34592) hydrogen bonds : bond 0.03226 ( 1167) hydrogen bonds : angle 4.49251 ( 3411) *********************** 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 292 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: A 432 LYS cc_start: 0.7766 (tptp) cc_final: 0.7531 (tptp) REVERT: A 468 ILE cc_start: 0.8675 (mm) cc_final: 0.8299 (mp) REVERT: A 576 CYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 432 LYS cc_start: 0.8496 (tppt) cc_final: 0.8247 (tptp) REVERT: B 460 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8067 (t0) REVERT: B 618 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 949 ASP cc_start: 0.7262 (m-30) cc_final: 0.6073 (p0) REVERT: C 475 ASN cc_start: 0.8495 (t0) cc_final: 0.7532 (p0) REVERT: C 591 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: C 643 ASP cc_start: 0.8086 (m-30) cc_final: 0.7819 (p0) REVERT: C 647 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7849 (tp30) REVERT: C 826 MET cc_start: 0.8655 (tpp) cc_final: 0.8405 (tpt) REVERT: C 896 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8750 (tttp) REVERT: D 423 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: D 482 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7813 (ttm110) REVERT: D 488 GLU cc_start: 0.7609 (tp30) cc_final: 0.7278 (tp30) REVERT: D 609 GLU cc_start: 0.8411 (tt0) cc_final: 0.7660 (tm-30) REVERT: D 686 GLU cc_start: 0.8165 (tp30) cc_final: 0.7876 (tp30) REVERT: D 766 MET cc_start: 0.8734 (ttt) cc_final: 0.8458 (ttp) REVERT: D 846 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6297 (tm-30) REVERT: E 588 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8139 (tt) REVERT: E 591 GLU cc_start: 0.7767 (pt0) cc_final: 0.7078 (pp20) REVERT: F 581 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7505 (tppt) REVERT: F 589 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7278 (pp) REVERT: F 665 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: F 897 GLU cc_start: 0.8448 (mp0) cc_final: 0.8070 (mp0) outliers start: 49 outliers final: 31 residues processed: 275 average time/residue: 0.6463 time to fit residues: 204.9134 Evaluate side-chains 268 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 LYS Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 686 GLU Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 289 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 157 optimal weight: 0.0870 chunk 116 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 315 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 711 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094219 restraints weight = 38203.770| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.31 r_work: 0.3150 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25543 Z= 0.125 Angle : 0.541 12.060 34592 Z= 0.267 Chirality : 0.041 0.335 3952 Planarity : 0.004 0.045 4439 Dihedral : 7.705 133.423 3617 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.81 % Allowed : 17.29 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3157 helix: 1.94 (0.13), residues: 1486 sheet: 0.64 (0.25), residues: 411 loop : -0.39 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 652 TYR 0.023 0.001 TYR F 623 PHE 0.022 0.001 PHE A 547 TRP 0.007 0.001 TRP F 470 HIS 0.005 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00293 (25543) covalent geometry : angle 0.54083 (34592) hydrogen bonds : bond 0.03286 ( 1167) hydrogen bonds : angle 4.50366 ( 3411) ********************** 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 282 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7577 (ttpt) REVERT: A 432 LYS cc_start: 0.7774 (tptp) cc_final: 0.7539 (tptp) REVERT: A 468 ILE cc_start: 0.8675 (mm) cc_final: 0.8301 (mp) REVERT: A 576 CYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8515 (p) REVERT: B 432 LYS cc_start: 0.8501 (tppt) cc_final: 0.8265 (tptp) REVERT: B 460 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8064 (t0) REVERT: B 618 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 717 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: B 949 ASP cc_start: 0.7252 (m-30) cc_final: 0.6067 (p0) REVERT: C 475 ASN cc_start: 0.8503 (t0) cc_final: 0.7543 (p0) REVERT: C 591 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7831 (mm-30) REVERT: C 643 ASP cc_start: 0.8102 (m-30) cc_final: 0.7820 (p0) REVERT: C 647 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7851 (tp30) REVERT: C 826 MET cc_start: 0.8672 (tpp) cc_final: 0.8422 (tpt) REVERT: C 896 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8754 (tttp) REVERT: D 423 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: D 482 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7888 (ttm110) REVERT: D 488 GLU cc_start: 0.7613 (tp30) cc_final: 0.7287 (tp30) REVERT: D 609 GLU cc_start: 0.8417 (tt0) cc_final: 0.7667 (tm-30) REVERT: D 686 GLU cc_start: 0.8186 (tp30) cc_final: 0.7901 (tp30) REVERT: D 766 MET cc_start: 0.8750 (ttt) cc_final: 0.8476 (ttp) REVERT: D 846 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6257 (tm-30) REVERT: E 588 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8138 (tt) REVERT: E 591 GLU cc_start: 0.7836 (pt0) cc_final: 0.7128 (pp20) REVERT: F 581 LYS cc_start: 0.7851 (mmtp) cc_final: 0.7505 (tppt) REVERT: F 589 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7275 (pp) REVERT: F 665 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: F 897 GLU cc_start: 0.8460 (mp0) cc_final: 0.8077 (mp0) outliers start: 49 outliers final: 34 residues processed: 267 average time/residue: 0.6708 time to fit residues: 206.1667 Evaluate side-chains 274 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 LYS Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 686 GLU Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain F residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 27 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 284 optimal weight: 1.9990 chunk 193 optimal weight: 0.0670 chunk 290 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 711 ASN F 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094217 restraints weight = 38285.853| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.32 r_work: 0.3142 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25543 Z= 0.134 Angle : 0.545 12.035 34592 Z= 0.269 Chirality : 0.041 0.329 3952 Planarity : 0.004 0.043 4439 Dihedral : 7.706 134.723 3617 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.95 % Allowed : 17.25 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3157 helix: 1.96 (0.13), residues: 1477 sheet: 0.66 (0.25), residues: 413 loop : -0.39 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 652 TYR 0.023 0.001 TYR F 623 PHE 0.028 0.001 PHE F 547 TRP 0.007 0.001 TRP F 470 HIS 0.005 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00316 (25543) covalent geometry : angle 0.54491 (34592) hydrogen bonds : bond 0.03367 ( 1167) hydrogen bonds : angle 4.51428 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9957.82 seconds wall clock time: 170 minutes 15.28 seconds (10215.28 seconds total)