Starting phenix.real_space_refine on Sat Sep 12 15:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kz4_0785/09_2026/6kz4_0785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kz4_0785/09_2026/6kz4_0785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kz4_0785/09_2026/6kz4_0785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kz4_0785/09_2026/6kz4_0785.map" model { file = "/net/cci-nas-00/data/ceres_data/6kz4_0785/09_2026/6kz4_0785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kz4_0785/09_2026/6kz4_0785.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 10614 2.51 5 N 2922 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16698 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.98, per 1000 atoms: 0.24 Number of scatterers: 16698 At special positions: 0 Unit cell: (105.07, 105.07, 114.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 3138 8.00 N 2922 7.00 C 10614 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: 1.52 Conformation dependent library (CDL) restraints added in 792.6 milliseconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 31 sheets defined 9.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'E' and resid 561 through 567 removed outlier: 3.798A pdb=" N ARG E 564 " --> pdb=" O PRO E 561 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN E 565 " --> pdb=" O GLU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 601 Processing helix chain 'E' and resid 626 through 632 removed outlier: 3.589A pdb=" N ALA E 630 " --> pdb=" O SER E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 715 removed outlier: 3.575A pdb=" N LEU E 715 " --> pdb=" O ASP E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.527A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 834 Processing helix chain 'F' and resid 626 through 632 removed outlier: 3.533A pdb=" N ALA F 630 " --> pdb=" O SER F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 715 removed outlier: 3.689A pdb=" N LEU F 715 " --> pdb=" O ASP F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 830 through 834 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 626 through 632 removed outlier: 3.643A pdb=" N ALA C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 removed outlier: 3.595A pdb=" N LEU C 715 " --> pdb=" O ASP C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.542A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 834 Processing helix chain 'C' and resid 867 through 871 Processing helix chain 'D' and resid 626 through 632 removed outlier: 3.541A pdb=" N ALA D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 830 through 834 Processing helix chain 'D' and resid 867 through 871 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.801A pdb=" N ARG A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.652A pdb=" N ALA A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 removed outlier: 3.568A pdb=" N LEU A 715 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.566A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.542A pdb=" N LEU B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 removed outlier: 3.525A pdb=" N ALA B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 4.235A pdb=" N LYS B 646 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 830 through 834 Processing sheet with id=AA1, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.820A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 555 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR E 545 " --> pdb=" O ASP E 556 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS E 558 " --> pdb=" O VAL E 543 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL E 543 " --> pdb=" O HIS E 558 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL E 532 " --> pdb=" O ILE E 603 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE E 605 " --> pdb=" O VAL E 532 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU E 534 " --> pdb=" O PHE E 605 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ASN E 607 " --> pdb=" O LEU E 534 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 583 through 584 Processing sheet with id=AA3, first strand: chain 'E' and resid 667 through 669 removed outlier: 6.489A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR E 718 " --> pdb=" O VAL E 699 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 734 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS E 640 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 702 through 704 removed outlier: 3.577A pdb=" N GLY E 707 " --> pdb=" O SER E 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 809 through 811 removed outlier: 6.215A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N PHE E 858 " --> pdb=" O SER E 749 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE E 751 " --> pdb=" O PHE E 858 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 553 through 559 removed outlier: 6.836A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL F 532 " --> pdb=" O ILE F 603 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE F 605 " --> pdb=" O VAL F 532 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 534 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASN F 607 " --> pdb=" O LEU F 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 667 through 669 removed outlier: 6.603A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 734 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS F 640 " --> pdb=" O LEU F 734 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 702 through 704 removed outlier: 3.512A pdb=" N SER F 704 " --> pdb=" O GLY F 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 747 through 748 removed outlier: 6.182A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL F 773 " --> pdb=" O SER F 795 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 766 " --> pdb=" O VAL F 773 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 747 through 748 removed outlier: 7.006A pdb=" N ILE F 751 " --> pdb=" O PHE F 858 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 521 removed outlier: 3.820A pdb=" N VAL C 517 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 555 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 532 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE C 605 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU C 534 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ASN C 607 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 583 through 584 Processing sheet with id=AB4, first strand: chain 'C' and resid 667 through 669 removed outlier: 6.540A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.643A pdb=" N GLY C 707 " --> pdb=" O SER C 704 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 809 through 811 removed outlier: 6.306A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N PHE C 858 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 751 " --> pdb=" O PHE C 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 518 through 521 removed outlier: 3.570A pdb=" N ILE D 555 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 605 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'D' and resid 667 through 669 removed outlier: 6.616A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR D 718 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 734 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS D 640 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 702 through 704 Processing sheet with id=AC2, first strand: chain 'D' and resid 747 through 748 removed outlier: 6.595A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER D 795 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY D 774 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 766 " --> pdb=" O VAL D 773 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 747 through 748 removed outlier: 7.001A pdb=" N ILE D 751 " --> pdb=" O PHE D 858 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.778A pdb=" N VAL A 517 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 555 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 545 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS A 558 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL A 543 " --> pdb=" O HIS A 558 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 532 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE A 605 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 534 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ASN A 607 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AC6, first strand: chain 'A' and resid 667 through 669 removed outlier: 6.529A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 696 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 734 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS A 640 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'A' and resid 838 through 839 removed outlier: 6.286A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 791 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A 779 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N MET A 789 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N PHE A 858 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 751 " --> pdb=" O PHE A 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 518 through 521 removed outlier: 3.601A pdb=" N PHE B 553 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 532 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE B 605 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 534 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ASN B 607 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 667 through 669 removed outlier: 6.625A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR B 718 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 734 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS B 640 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 748 removed outlier: 6.666A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 795 " --> pdb=" O GLY B 774 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY B 774 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 766 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 748 removed outlier: 6.981A pdb=" N ILE B 751 " --> pdb=" O PHE B 858 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5548 1.34 - 1.45: 2085 1.45 - 1.57: 9353 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 17034 Sorted by residual: bond pdb=" C SER A 531 " pdb=" N VAL A 532 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.24e-02 6.50e+03 1.41e+00 bond pdb=" CA VAL D 802 " pdb=" CB VAL D 802 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.39e+00 bond pdb=" CA VAL A 802 " pdb=" CB VAL A 802 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.34e+00 bond pdb=" CB PHE E 840 " pdb=" CG PHE E 840 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.27e+00 bond pdb=" CB PRO B 594 " pdb=" CG PRO B 594 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.91e-01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 22385 1.54 - 3.08: 642 3.08 - 4.63: 97 4.63 - 6.17: 12 6.17 - 7.71: 6 Bond angle restraints: 23142 Sorted by residual: angle pdb=" N VAL F 773 " pdb=" CA VAL F 773 " pdb=" C VAL F 773 " ideal model delta sigma weight residual 113.71 108.81 4.90 9.50e-01 1.11e+00 2.66e+01 angle pdb=" N ASN B 551 " pdb=" CA ASN B 551 " pdb=" C ASN B 551 " ideal model delta sigma weight residual 114.75 108.70 6.05 1.26e+00 6.30e-01 2.31e+01 angle pdb=" N ILE B 660 " pdb=" CA ILE B 660 " pdb=" C ILE B 660 " ideal model delta sigma weight residual 112.96 108.45 4.51 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N ASN F 551 " pdb=" CA ASN F 551 " pdb=" C ASN F 551 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N LEU B 595 " pdb=" CA LEU B 595 " pdb=" C LEU B 595 " ideal model delta sigma weight residual 114.62 110.24 4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 23137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9268 17.91 - 35.81: 715 35.81 - 53.72: 107 53.72 - 71.62: 36 71.62 - 89.53: 14 Dihedral angle restraints: 10140 sinusoidal: 3954 harmonic: 6186 Sorted by residual: dihedral pdb=" CA ARG F 536 " pdb=" C ARG F 536 " pdb=" N LYS F 537 " pdb=" CA LYS F 537 " ideal model delta harmonic sigma weight residual 180.00 135.62 44.38 0 5.00e+00 4.00e-02 7.88e+01 dihedral pdb=" CA ARG B 536 " pdb=" C ARG B 536 " pdb=" N LYS B 537 " pdb=" CA LYS B 537 " ideal model delta harmonic sigma weight residual 180.00 137.95 42.05 0 5.00e+00 4.00e-02 7.07e+01 dihedral pdb=" CA ARG D 536 " pdb=" C ARG D 536 " pdb=" N LYS D 537 " pdb=" CA LYS D 537 " ideal model delta harmonic sigma weight residual 180.00 139.19 40.81 0 5.00e+00 4.00e-02 6.66e+01 ... (remaining 10137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1756 0.040 - 0.081: 623 0.081 - 0.121: 242 0.121 - 0.161: 36 0.161 - 0.202: 1 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CB ILE E 750 " pdb=" CA ILE E 750 " pdb=" CG1 ILE E 750 " pdb=" CG2 ILE E 750 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE B 653 " pdb=" N ILE B 653 " pdb=" C ILE B 653 " pdb=" CB ILE B 653 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE E 653 " pdb=" N ILE E 653 " pdb=" C ILE E 653 " pdb=" CB ILE E 653 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 2655 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 547 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 548 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 536 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C ARG A 536 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 536 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 537 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 536 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C ARG E 536 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG E 536 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS E 537 " 0.009 2.00e-02 2.50e+03 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 832 2.72 - 3.26: 16099 3.26 - 3.81: 25168 3.81 - 4.35: 32785 4.35 - 4.90: 56650 Nonbonded interactions: 131534 Sorted by model distance: nonbonded pdb=" OH TYR F 744 " pdb=" OE1 GLU F 772 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR D 744 " pdb=" OE2 GLU D 772 " model vdw 2.193 3.040 nonbonded pdb=" O HIS A 710 " pdb=" OG1 THR A 713 " model vdw 2.237 3.040 nonbonded pdb=" O HIS B 710 " pdb=" OG1 THR B 713 " model vdw 2.262 3.040 nonbonded pdb=" O HIS F 710 " pdb=" OG1 THR F 713 " model vdw 2.264 3.040 ... (remaining 131529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.820 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.005 0.050 17034 Z= 0.223 Angle : 0.643 7.712 23142 Z= 0.372 Chirality : 0.047 0.202 2658 Planarity : 0.003 0.045 3006 Dihedral : 13.568 89.529 6204 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.51 (0.15), residues: 2184 helix: -4.80 (0.15), residues: 186 sheet: -3.15 (0.16), residues: 762 loop : -2.59 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 793 TYR 0.009 0.001 TYR D 535 PHE 0.025 0.002 PHE A 840 TRP 0.021 0.002 TRP F 809 HIS 0.002 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (17034) covalent geometry : angle 0.64275 / 0.37 (23142) hydrogen bonds : bond 0.26660 / 18.12 ( 436) hydrogen bonds : angle 11.01387 / 7.58 ( 957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.520 Fit side-chains REVERT: F 673 ASN cc_start: 0.8075 (m110) cc_final: 0.7517 (m-40) REVERT: F 814 TYR cc_start: 0.8685 (m-80) cc_final: 0.8402 (m-80) REVERT: F 835 ARG cc_start: 0.6884 (mtm110) cc_final: 0.6379 (ptt90) REVERT: C 798 TYR cc_start: 0.9336 (m-80) cc_final: 0.9071 (m-80) REVERT: D 779 MET cc_start: 0.8634 (mtm) cc_final: 0.8149 (mtm) REVERT: D 870 GLU cc_start: 0.7747 (pp20) cc_final: 0.7504 (pp20) REVERT: B 835 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6650 (ptm-80) outliers start: 0 outliers final: 2 residues processed: 221 average time/residue: 0.7429 time to fit residues: 180.0817 Evaluate side-chains 127 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain F residue 622 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.2980 chunk 212 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 662 GLN E 716 GLN F 673 ASN F 702 GLN F 716 GLN ** F 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 GLN C 716 GLN C 720 ASN C 831 ASN C 857 HIS D 673 ASN D 716 GLN A 662 GLN A 716 GLN A 720 ASN B 710 HIS B 716 GLN B 800 HIS B 832 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.089676 restraints weight = 24634.676| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.74 r_work: 0.2919 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17034 Z= 0.149 Angle : 0.594 7.478 23142 Z= 0.310 Chirality : 0.048 0.170 2658 Planarity : 0.004 0.036 3006 Dihedral : 5.238 41.863 2386 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.79 % Allowed : 13.31 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.17), residues: 2184 helix: -4.14 (0.27), residues: 156 sheet: -2.60 (0.16), residues: 792 loop : -2.03 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 672 TYR 0.010 0.001 TYR B 535 PHE 0.019 0.002 PHE B 840 TRP 0.014 0.002 TRP D 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (17034) covalent geometry : angle 0.59362 / 0.31 (23142) hydrogen bonds : bond 0.04320 / 2.92 ( 436) hydrogen bonds : angle 7.80714 / 5.30 ( 957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: F 835 ARG cc_start: 0.6962 (mtm110) cc_final: 0.6634 (ptt90) REVERT: C 798 TYR cc_start: 0.9394 (m-80) cc_final: 0.9124 (m-80) REVERT: D 523 THR cc_start: 0.8861 (p) cc_final: 0.8660 (t) REVERT: D 560 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8156 (mtpt) REVERT: D 751 ILE cc_start: 0.9262 (mt) cc_final: 0.9039 (mp) REVERT: D 779 MET cc_start: 0.8861 (mtm) cc_final: 0.8613 (mtm) REVERT: B 725 ARG cc_start: 0.8281 (mmt180) cc_final: 0.8030 (mmt90) REVERT: B 835 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6489 (ptt90) outliers start: 49 outliers final: 26 residues processed: 173 average time/residue: 0.5769 time to fit residues: 112.3069 Evaluate side-chains 146 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 868 TRP Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 620 LYS Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 201 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 209 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 720 ASN C 831 ASN ** D 720 ASN ** 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 = 0.3384 r_free = 0.3384 target = 0.113108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089908 restraints weight = 24857.111| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.72 r_work: 0.2902 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17034 Z= 0.177 Angle : 0.590 7.269 23142 Z= 0.306 Chirality : 0.048 0.172 2658 Planarity : 0.003 0.040 3006 Dihedral : 5.130 43.304 2382 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.53 % Allowed : 15.47 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.17), residues: 2184 helix: -3.87 (0.30), residues: 156 sheet: -2.41 (0.17), residues: 786 loop : -1.74 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 672 TYR 0.010 0.001 TYR F 798 PHE 0.017 0.002 PHE D 840 TRP 0.016 0.002 TRP D 809 HIS 0.002 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (17034) covalent geometry : angle 0.59041 / 0.31 (23142) hydrogen bonds : bond 0.03808 / 2.59 ( 436) hydrogen bonds : angle 7.15661 / 4.84 ( 957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: F 798 TYR cc_start: 0.9103 (m-80) cc_final: 0.8795 (m-80) REVERT: F 835 ARG cc_start: 0.6996 (mtm110) cc_final: 0.6670 (ptt90) REVERT: C 779 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8847 (mtp) REVERT: C 798 TYR cc_start: 0.9458 (m-80) cc_final: 0.9194 (m-80) REVERT: D 534 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8370 (mp) REVERT: D 620 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.7082 (pttt) REVERT: D 660 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8901 (mp) REVERT: D 779 MET cc_start: 0.9089 (mtm) cc_final: 0.8856 (mtm) REVERT: A 779 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8690 (mtp) REVERT: B 725 ARG cc_start: 0.8544 (mmt180) cc_final: 0.8281 (mmt90) REVERT: B 835 ARG cc_start: 0.7047 (mtm110) cc_final: 0.6383 (ptt90) outliers start: 62 outliers final: 32 residues processed: 173 average time/residue: 0.5378 time to fit residues: 105.2697 Evaluate side-chains 149 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 620 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 10 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 164 optimal weight: 0.0770 chunk 177 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 831 ASN ** D 720 ASN ** 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 = 0.3387 r_free = 0.3387 target = 0.113464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090296 restraints weight = 24635.727| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.71 r_work: 0.2906 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17034 Z= 0.157 Angle : 0.573 8.603 23142 Z= 0.296 Chirality : 0.047 0.169 2658 Planarity : 0.003 0.032 3006 Dihedral : 4.985 43.206 2382 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.53 % Allowed : 17.29 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.17), residues: 2184 helix: -3.62 (0.32), residues: 156 sheet: -2.25 (0.17), residues: 786 loop : -1.57 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 672 TYR 0.009 0.001 TYR F 798 PHE 0.014 0.002 PHE B 553 TRP 0.015 0.002 TRP D 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (17034) covalent geometry : angle 0.57335 / 0.30 (23142) hydrogen bonds : bond 0.03355 / 2.31 ( 436) hydrogen bonds : angle 6.81728 / 4.61 ( 957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8781 (pt0) cc_final: 0.8496 (tt0) REVERT: E 809 TRP cc_start: 0.8528 (OUTLIER) cc_final: 0.8274 (p-90) REVERT: F 627 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: F 798 TYR cc_start: 0.9093 (m-80) cc_final: 0.8718 (m-80) REVERT: F 809 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.7848 (p-90) REVERT: F 835 ARG cc_start: 0.7050 (mtm110) cc_final: 0.6766 (ptt90) REVERT: F 864 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: C 779 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8732 (mtp) REVERT: C 798 TYR cc_start: 0.9446 (m-80) cc_final: 0.9187 (m-80) REVERT: D 534 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8322 (mp) REVERT: D 560 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8260 (mtpt) REVERT: D 620 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7074 (pttt) REVERT: D 627 GLU cc_start: 0.8025 (tp30) cc_final: 0.7492 (tp30) REVERT: D 779 MET cc_start: 0.9100 (mtm) cc_final: 0.8846 (mtm) REVERT: D 870 GLU cc_start: 0.8398 (pp20) cc_final: 0.8183 (pp20) REVERT: A 779 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8726 (mtp) REVERT: A 809 TRP cc_start: 0.8803 (OUTLIER) cc_final: 0.7533 (p-90) REVERT: A 840 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7307 (t80) REVERT: B 523 THR cc_start: 0.8926 (p) cc_final: 0.8717 (t) REVERT: B 627 GLU cc_start: 0.8478 (tp30) cc_final: 0.7954 (tp30) REVERT: B 716 GLN cc_start: 0.8929 (tt0) cc_final: 0.8678 (tt0) REVERT: B 725 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8310 (mmt90) REVERT: B 783 THR cc_start: 0.9004 (p) cc_final: 0.8755 (t) REVERT: B 835 ARG cc_start: 0.7093 (mtm110) cc_final: 0.6500 (ptt90) outliers start: 62 outliers final: 33 residues processed: 163 average time/residue: 0.5394 time to fit residues: 99.6822 Evaluate side-chains 155 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 620 LYS Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 131 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 799 GLN C 831 ASN D 710 HIS D 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088274 restraints weight = 24669.456| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.70 r_work: 0.2874 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17034 Z= 0.216 Angle : 0.610 8.469 23142 Z= 0.317 Chirality : 0.049 0.188 2658 Planarity : 0.003 0.032 3006 Dihedral : 5.189 45.845 2382 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.87 % Allowed : 18.03 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.86 (0.18), residues: 2184 helix: -3.47 (0.33), residues: 156 sheet: -2.13 (0.17), residues: 807 loop : -1.42 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 672 TYR 0.010 0.001 TYR F 798 PHE 0.022 0.002 PHE B 553 TRP 0.017 0.002 TRP D 809 HIS 0.003 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (17034) covalent geometry : angle 0.60966 / 0.32 (23142) hydrogen bonds : bond 0.03542 / 2.42 ( 436) hydrogen bonds : angle 6.85980 / 4.64 ( 957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8801 (pt0) cc_final: 0.8523 (tt0) REVERT: E 809 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.7948 (p-90) REVERT: F 627 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: F 798 TYR cc_start: 0.9158 (m-80) cc_final: 0.8756 (m-80) REVERT: F 809 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (p-90) REVERT: F 835 ARG cc_start: 0.7010 (mtm110) cc_final: 0.6682 (ptt90) REVERT: F 864 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: C 595 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9026 (tm) REVERT: C 779 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8708 (mtp) REVERT: C 798 TYR cc_start: 0.9469 (m-80) cc_final: 0.9209 (m-80) REVERT: C 866 LYS cc_start: 0.8477 (pmtt) cc_final: 0.8273 (ptmm) REVERT: D 627 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: D 660 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8920 (mp) REVERT: D 779 MET cc_start: 0.9086 (mtm) cc_final: 0.8832 (mtm) REVERT: D 809 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.8235 (p-90) REVERT: D 870 GLU cc_start: 0.8398 (pp20) cc_final: 0.8178 (pp20) REVERT: A 779 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8571 (mtp) REVERT: A 840 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7436 (t80) REVERT: B 523 THR cc_start: 0.8980 (p) cc_final: 0.8739 (t) REVERT: B 627 GLU cc_start: 0.8504 (tp30) cc_final: 0.8008 (tp30) REVERT: B 716 GLN cc_start: 0.8969 (tt0) cc_final: 0.8731 (tt0) REVERT: B 725 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8290 (mmt90) REVERT: B 783 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8808 (t) REVERT: B 835 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6532 (ptt90) outliers start: 68 outliers final: 39 residues processed: 161 average time/residue: 0.5113 time to fit residues: 93.5651 Evaluate side-chains 159 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 159 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.1281 > 50:) chunk 152 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088600 restraints weight = 24715.084| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.71 r_work: 0.2879 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17034 Z= 0.197 Angle : 0.592 8.394 23142 Z= 0.307 Chirality : 0.048 0.198 2658 Planarity : 0.003 0.028 3006 Dihedral : 5.144 45.591 2382 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.75 % Allowed : 18.77 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.72 (0.18), residues: 2184 helix: -3.31 (0.34), residues: 156 sheet: -2.01 (0.17), residues: 801 loop : -1.36 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 672 TYR 0.009 0.001 TYR F 798 PHE 0.020 0.002 PHE B 553 TRP 0.016 0.002 TRP D 809 HIS 0.002 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (17034) covalent geometry : angle 0.59216 / 0.31 (23142) hydrogen bonds : bond 0.03375 / 2.32 ( 436) hydrogen bonds : angle 6.70687 / 4.54 ( 957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8787 (pt0) cc_final: 0.8510 (tt0) REVERT: E 809 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.7874 (p-90) REVERT: F 798 TYR cc_start: 0.9144 (m-80) cc_final: 0.8731 (m-80) REVERT: F 809 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.8158 (p-90) REVERT: F 835 ARG cc_start: 0.7056 (mtm110) cc_final: 0.6765 (ptt90) REVERT: F 864 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: C 595 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9034 (tm) REVERT: C 779 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: C 798 TYR cc_start: 0.9458 (m-80) cc_final: 0.9184 (m-80) REVERT: D 560 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8300 (mtpt) REVERT: D 627 GLU cc_start: 0.8074 (tp30) cc_final: 0.7480 (tp30) REVERT: D 660 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8915 (mp) REVERT: D 779 MET cc_start: 0.9096 (mtm) cc_final: 0.8791 (mtm) REVERT: D 809 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.8126 (p-90) REVERT: D 840 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7405 (t80) REVERT: A 651 MET cc_start: 0.9447 (ttp) cc_final: 0.9201 (ttp) REVERT: A 779 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (mtp) REVERT: A 809 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.7486 (p-90) REVERT: A 840 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 523 THR cc_start: 0.8951 (p) cc_final: 0.8703 (t) REVERT: B 627 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: B 716 GLN cc_start: 0.8965 (tt0) cc_final: 0.8680 (tt0) REVERT: B 725 ARG cc_start: 0.8548 (mmt180) cc_final: 0.8286 (mmt90) REVERT: B 783 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8815 (t) REVERT: B 835 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6669 (ptt90) outliers start: 66 outliers final: 39 residues processed: 160 average time/residue: 0.4934 time to fit residues: 90.1404 Evaluate side-chains 164 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 206 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 193 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090791 restraints weight = 24472.228| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.70 r_work: 0.2913 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17034 Z= 0.129 Angle : 0.554 8.498 23142 Z= 0.286 Chirality : 0.047 0.224 2658 Planarity : 0.003 0.027 3006 Dihedral : 4.867 43.115 2382 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.36 % Allowed : 19.34 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.53 (0.18), residues: 2184 helix: -3.13 (0.35), residues: 156 sheet: -1.91 (0.17), residues: 789 loop : -1.24 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 631 TYR 0.009 0.001 TYR B 624 PHE 0.013 0.002 PHE C 605 TRP 0.015 0.001 TRP D 809 HIS 0.001 0.000 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17034) covalent geometry : angle 0.55394 / 0.29 (23142) hydrogen bonds : bond 0.03080 / 2.12 ( 436) hydrogen bonds : angle 6.47479 / 4.39 ( 957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 127 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8803 (pt0) cc_final: 0.8526 (tt0) REVERT: E 809 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.8000 (p-90) REVERT: E 835 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7239 (ptt90) REVERT: F 798 TYR cc_start: 0.9071 (m-80) cc_final: 0.8671 (m-80) REVERT: F 809 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.7675 (p-90) REVERT: F 835 ARG cc_start: 0.7081 (mtm110) cc_final: 0.6824 (ptt90) REVERT: F 864 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: C 595 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8991 (tm) REVERT: C 655 TYR cc_start: 0.9437 (t80) cc_final: 0.8842 (t80) REVERT: C 779 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8806 (mtp) REVERT: C 798 TYR cc_start: 0.9440 (m-80) cc_final: 0.9167 (m-80) REVERT: D 534 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8333 (mp) REVERT: D 560 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8233 (mtpt) REVERT: D 627 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: D 660 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8856 (mp) REVERT: D 779 MET cc_start: 0.9100 (mtm) cc_final: 0.8728 (mtm) REVERT: D 809 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.8148 (p-90) REVERT: A 809 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.7436 (p-90) REVERT: A 840 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7467 (t80) REVERT: B 523 THR cc_start: 0.8906 (p) cc_final: 0.8674 (t) REVERT: B 627 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: B 716 GLN cc_start: 0.8931 (tt0) cc_final: 0.8643 (tt0) REVERT: B 725 ARG cc_start: 0.8502 (mmt180) cc_final: 0.8259 (mmt90) REVERT: B 830 PHE cc_start: 0.3770 (OUTLIER) cc_final: 0.3477 (m-80) REVERT: B 835 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6669 (ptt90) outliers start: 59 outliers final: 31 residues processed: 162 average time/residue: 0.4931 time to fit residues: 91.3899 Evaluate side-chains 158 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 799 GLN A 857 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.087163 restraints weight = 24961.975| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.70 r_work: 0.2857 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17034 Z= 0.261 Angle : 0.642 8.181 23142 Z= 0.332 Chirality : 0.050 0.227 2658 Planarity : 0.004 0.030 3006 Dihedral : 5.276 48.196 2382 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.92 % Allowed : 19.40 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.53 (0.18), residues: 2184 helix: -3.11 (0.35), residues: 156 sheet: -1.90 (0.17), residues: 807 loop : -1.23 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 536 TYR 0.011 0.001 TYR A 718 PHE 0.024 0.002 PHE B 553 TRP 0.018 0.002 TRP D 809 HIS 0.003 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 (17034) covalent geometry : angle 0.64199 / 0.33 (23142) hydrogen bonds : bond 0.03584 / 2.45 ( 436) hydrogen bonds : angle 6.74976 / 4.57 ( 957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 110 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8783 (pt0) cc_final: 0.8512 (tt0) REVERT: E 767 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9274 (mt) REVERT: E 809 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.8332 (p-90) REVERT: F 798 TYR cc_start: 0.9198 (m-80) cc_final: 0.8700 (m-80) REVERT: F 809 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.8111 (p-90) REVERT: F 835 ARG cc_start: 0.7007 (mtm110) cc_final: 0.6660 (ptt90) REVERT: F 864 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: C 595 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9086 (tm) REVERT: C 779 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8704 (mtp) REVERT: C 798 TYR cc_start: 0.9470 (m-80) cc_final: 0.9147 (m-80) REVERT: C 866 LYS cc_start: 0.8478 (pmtt) cc_final: 0.8232 (ptmm) REVERT: D 560 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8323 (mtpt) REVERT: D 627 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7523 (tp30) REVERT: D 660 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8937 (mp) REVERT: D 779 MET cc_start: 0.9113 (mtm) cc_final: 0.8640 (mtm) REVERT: D 809 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.8257 (p-90) REVERT: D 840 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7408 (t80) REVERT: A 712 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8386 (p0) REVERT: A 779 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8791 (mpp) REVERT: A 840 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7355 (t80) REVERT: A 860 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9141 (mm) REVERT: B 523 THR cc_start: 0.9000 (p) cc_final: 0.8734 (t) REVERT: B 627 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: B 716 GLN cc_start: 0.8992 (tt0) cc_final: 0.8713 (tt0) REVERT: B 725 ARG cc_start: 0.8557 (mmt180) cc_final: 0.8280 (mmt90) REVERT: B 835 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6673 (ptt90) outliers start: 69 outliers final: 40 residues processed: 156 average time/residue: 0.5135 time to fit residues: 91.4496 Evaluate side-chains 159 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 200 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 191 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 799 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089330 restraints weight = 24701.912| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.74 r_work: 0.2904 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17034 Z= 0.134 Angle : 0.574 9.212 23142 Z= 0.294 Chirality : 0.047 0.236 2658 Planarity : 0.003 0.025 3006 Dihedral : 4.924 45.973 2382 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.19 % Allowed : 20.42 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.41 (0.18), residues: 2184 helix: -2.93 (0.37), residues: 156 sheet: -1.85 (0.18), residues: 789 loop : -1.16 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 672 TYR 0.009 0.001 TYR B 624 PHE 0.021 0.002 PHE C 830 TRP 0.016 0.001 TRP D 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (17034) covalent geometry : angle 0.57394 / 0.29 (23142) hydrogen bonds : bond 0.03052 / 2.09 ( 436) hydrogen bonds : angle 6.43853 / 4.37 ( 957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8632 (pt0) cc_final: 0.8376 (tt0) REVERT: E 767 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9140 (mt) REVERT: E 809 TRP cc_start: 0.8415 (OUTLIER) cc_final: 0.7749 (p-90) REVERT: E 835 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7299 (ptt90) REVERT: E 866 LYS cc_start: 0.8354 (pmtt) cc_final: 0.8065 (ptpp) REVERT: F 547 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7622 (ptt-90) REVERT: F 798 TYR cc_start: 0.9053 (m-80) cc_final: 0.8653 (m-80) REVERT: F 809 TRP cc_start: 0.8308 (OUTLIER) cc_final: 0.7188 (p-90) REVERT: F 835 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6836 (ptt90) REVERT: C 595 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (tm) REVERT: C 655 TYR cc_start: 0.9418 (t80) cc_final: 0.8892 (t80) REVERT: C 779 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8670 (mtp) REVERT: C 798 TYR cc_start: 0.9408 (m-80) cc_final: 0.9107 (m-80) REVERT: D 560 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8210 (mtpt) REVERT: D 627 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: D 660 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8805 (mp) REVERT: D 779 MET cc_start: 0.8991 (mtm) cc_final: 0.8683 (mtm) REVERT: D 809 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7944 (p-90) REVERT: A 651 MET cc_start: 0.9361 (ttp) cc_final: 0.9027 (ttp) REVERT: A 712 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8220 (p0) REVERT: A 809 TRP cc_start: 0.8617 (OUTLIER) cc_final: 0.7460 (p-90) REVERT: A 840 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7159 (t80) REVERT: B 523 THR cc_start: 0.8845 (p) cc_final: 0.8609 (t) REVERT: B 627 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: B 716 GLN cc_start: 0.8812 (tt0) cc_final: 0.8528 (tt0) REVERT: B 725 ARG cc_start: 0.8275 (mmt180) cc_final: 0.8064 (mmt90) REVERT: B 835 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6752 (ptt90) outliers start: 56 outliers final: 33 residues processed: 158 average time/residue: 0.5045 time to fit residues: 91.2585 Evaluate side-chains 165 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 835 ARG Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 186 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088176 restraints weight = 24690.279| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.73 r_work: 0.2887 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17034 Z= 0.171 Angle : 0.597 8.537 23142 Z= 0.305 Chirality : 0.048 0.249 2658 Planarity : 0.003 0.028 3006 Dihedral : 4.968 46.090 2382 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.96 % Allowed : 20.88 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.39 (0.18), residues: 2184 helix: -2.94 (0.37), residues: 156 sheet: -1.79 (0.17), residues: 807 loop : -1.16 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 672 TYR 0.009 0.001 TYR B 624 PHE 0.023 0.002 PHE C 830 TRP 0.016 0.002 TRP D 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (17034) covalent geometry : angle 0.59747 / 0.31 (23142) hydrogen bonds : bond 0.03230 / 2.22 ( 436) hydrogen bonds : angle 6.49857 / 4.41 ( 957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: E 542 GLU cc_start: 0.8834 (pt0) cc_final: 0.8560 (tt0) REVERT: E 767 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9237 (mt) REVERT: E 809 TRP cc_start: 0.8574 (OUTLIER) cc_final: 0.7835 (p-90) REVERT: E 866 LYS cc_start: 0.8399 (pmtt) cc_final: 0.8099 (ptpp) REVERT: F 547 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7876 (ptt-90) REVERT: F 798 TYR cc_start: 0.9114 (m-80) cc_final: 0.8706 (m-80) REVERT: F 835 ARG cc_start: 0.7100 (mtm110) cc_final: 0.6799 (ptt90) REVERT: C 595 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9044 (tm) REVERT: C 655 TYR cc_start: 0.9461 (t80) cc_final: 0.9023 (t80) REVERT: C 779 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8694 (mtp) REVERT: C 798 TYR cc_start: 0.9448 (m-80) cc_final: 0.9150 (m-80) REVERT: D 560 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8274 (mtpt) REVERT: D 627 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: D 660 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8891 (mp) REVERT: D 779 MET cc_start: 0.9130 (mtm) cc_final: 0.8818 (mtm) REVERT: D 809 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.8191 (p-90) REVERT: A 651 MET cc_start: 0.9440 (ttp) cc_final: 0.9135 (ttp) REVERT: A 712 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8278 (p0) REVERT: A 779 MET cc_start: 0.9072 (mtm) cc_final: 0.8835 (mpp) REVERT: A 809 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.7581 (p-90) REVERT: A 840 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7373 (t80) REVERT: B 627 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 716 GLN cc_start: 0.8935 (tt0) cc_final: 0.8662 (tt0) REVERT: B 725 ARG cc_start: 0.8556 (mmt180) cc_final: 0.8282 (mmt90) REVERT: B 835 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6700 (ptt90) outliers start: 52 outliers final: 35 residues processed: 154 average time/residue: 0.4787 time to fit residues: 84.5052 Evaluate side-chains 160 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 36 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 165 optimal weight: 0.0010 chunk 194 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.0370 overall best weight: 0.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091134 restraints weight = 24468.748| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.71 r_work: 0.2918 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17034 Z= 0.127 Angle : 0.572 8.800 23142 Z= 0.291 Chirality : 0.047 0.254 2658 Planarity : 0.003 0.023 3006 Dihedral : 4.807 44.511 2382 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.79 % Allowed : 21.22 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.34 (0.18), residues: 2184 helix: -2.87 (0.37), residues: 156 sheet: -1.74 (0.18), residues: 801 loop : -1.14 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 672 TYR 0.009 0.001 TYR B 624 PHE 0.023 0.001 PHE C 830 TRP 0.016 0.001 TRP D 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17034) covalent geometry : angle 0.57192 / 0.29 (23142) hydrogen bonds : bond 0.02995 / 2.05 ( 436) hydrogen bonds : angle 6.35786 / 4.32 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.82 seconds wall clock time: 78 minutes 32.44 seconds (4712.44 seconds total)