Starting phenix.real_space_refine on Sun Aug 24 03:51:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kz4_0785/08_2025/6kz4_0785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kz4_0785/08_2025/6kz4_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kz4_0785/08_2025/6kz4_0785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kz4_0785/08_2025/6kz4_0785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kz4_0785/08_2025/6kz4_0785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kz4_0785/08_2025/6kz4_0785.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.58, per 1000 atoms: 0.27 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: 1.56 Conformation dependent library (CDL) restraints added in 869.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.98 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: 3.38 Time building geometry restraints manager: 2.05 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: 4.620 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: 0.050 Set scattering table: 0.040 Process input model: 18.280 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 aren 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 covalent geometry : bond 0.00503 (17034) covalent geometry : angle 0.64275 (23142) hydrogen bonds : bond 0.26660 ( 436) hydrogen bonds : angle 11.01387 ( 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 : 0.676 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: 0.8148 (mtm) REVERT: D 870 GLU cc_start: 0.7748 (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: 0.6682 time to fit residues: 161.7292 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 : 0.426 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8440 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 aren 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 covalent geometry : bond 0.00344 (17034) covalent geometry : angle 0.59362 (23142) hydrogen bonds : bond 0.04320 ( 436) hydrogen bonds : angle 7.80714 ( 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 : 0.469 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: 0.8280 (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: 0.5216 time to fit residues: 101.1465 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 : 0.638 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8567 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 aren 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 covalent geometry : bond 0.00415 (17034) covalent geometry : angle 0.59041 (23142) hydrogen bonds : bond 0.03808 ( 436) hydrogen bonds : angle 7.15661 ( 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 : 0.665 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: 0.4820 time to fit residues: 94.2325 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 : 0.695 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8568 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 aren 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 covalent geometry : bond 0.00368 (17034) covalent geometry : angle 0.57335 (23142) hydrogen bonds : bond 0.03355 ( 436) hydrogen bonds : angle 6.81728 ( 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 : 0.635 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: 0.7849 (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: 0.4906 time to fit residues: 90.4898 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 : 0.482 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8593 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 aren 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 covalent geometry : bond 0.00509 (17034) covalent geometry : angle 0.60966 (23142) hydrogen bonds : bond 0.03542 ( 436) hydrogen bonds : angle 6.85980 ( 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 : 0.656 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: 0.6681 (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: 0.8867 (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: 0.7106 (mtm110) cc_final: 0.6532 (ptt90) outliers start: 68 outliers final: 39 residues processed: 161 average time/residue: 0.5159 time to fit residues: 94.3395 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 : 0.495 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1281 > 50: distance: 66 - 71: 34.344 distance: 71 - 72: 39.602 distance: 72 - 73: 5.914 distance: 73 - 74: 20.454 distance: 73 - 75: 7.224 distance: 75 - 76: 39.100 distance: 75 - 210: 36.775 distance: 76 - 77: 16.616 distance: 76 - 79: 24.410 distance: 77 - 78: 11.844 distance: 77 - 84: 31.745 distance: 78 - 207: 22.464 distance: 79 - 80: 25.336 distance: 80 - 81: 37.408 distance: 81 - 82: 18.114 distance: 81 - 83: 29.041 distance: 84 - 85: 25.102 distance: 85 - 86: 30.324 distance: 85 - 88: 27.080 distance: 86 - 87: 17.886 distance: 86 - 92: 12.490 distance: 88 - 89: 17.192 distance: 88 - 90: 10.940 distance: 92 - 93: 15.778 distance: 93 - 94: 13.855 distance: 93 - 96: 12.465 distance: 94 - 95: 20.241 distance: 94 - 101: 20.965 distance: 96 - 97: 12.443 distance: 97 - 98: 8.341 distance: 98 - 99: 6.159 distance: 98 - 100: 14.538 distance: 101 - 102: 13.177 distance: 102 - 103: 23.930 distance: 102 - 105: 11.003 distance: 103 - 104: 32.771 distance: 103 - 108: 19.141 distance: 105 - 107: 14.302 distance: 108 - 109: 12.772 distance: 109 - 110: 35.667 distance: 109 - 112: 20.508 distance: 110 - 111: 33.287 distance: 110 - 116: 31.216 distance: 112 - 113: 23.276 distance: 113 - 114: 28.113 distance: 113 - 115: 15.165 distance: 116 - 117: 31.482 distance: 116 - 183: 11.661 distance: 117 - 118: 32.357 distance: 117 - 120: 24.153 distance: 118 - 119: 30.593 distance: 118 - 124: 27.008 distance: 119 - 180: 19.041 distance: 120 - 121: 16.996 distance: 121 - 122: 4.385 distance: 121 - 123: 18.902 distance: 124 - 125: 23.464 distance: 125 - 126: 33.995 distance: 125 - 128: 19.646 distance: 126 - 127: 32.267 distance: 126 - 132: 23.157 distance: 128 - 129: 5.889 distance: 129 - 130: 9.918 distance: 129 - 131: 11.752 distance: 132 - 133: 20.082 distance: 132 - 170: 10.471 distance: 133 - 134: 19.788 distance: 133 - 136: 12.461 distance: 134 - 135: 25.674 distance: 134 - 140: 17.862 distance: 135 - 167: 20.668 distance: 136 - 137: 18.257 distance: 136 - 138: 15.383 distance: 137 - 139: 21.231 distance: 140 - 141: 24.025 distance: 141 - 142: 24.326 distance: 141 - 144: 26.225 distance: 142 - 143: 9.921 distance: 142 - 147: 15.858 distance: 144 - 145: 11.819 distance: 144 - 146: 14.507