Starting phenix.real_space_refine on Sun May 18 13:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss9_40748/05_2025/8ss9_40748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss9_40748/05_2025/8ss9_40748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss9_40748/05_2025/8ss9_40748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss9_40748/05_2025/8ss9_40748.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss9_40748/05_2025/8ss9_40748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss9_40748/05_2025/8ss9_40748.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.179 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 S 104 5.16 5 Na 2 4.78 5 C 10718 2.51 5 N 2540 2.21 5 O 2929 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "C" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 230 Unusual residues: {' NA': 1, '6ZP': 1, 'CLR': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Unusual residues: {' NA': 1, '6ZP': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'6ZP': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 10.98, per 1000 atoms: 0.67 Number of scatterers: 16319 At special positions: 0 Unit cell: (117.475, 132.275, 134.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 104 16.00 P 14 15.00 Na 2 11.00 F 12 9.00 O 2929 8.00 N 2540 7.00 C 10718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 56.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.975A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.539A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.608A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.761A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.863A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.532A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.789A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.627A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.534A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.800A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.503A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 874 removed outlier: 3.797A pdb=" N GLN A 874 " --> pdb=" O PRO A 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 871 through 874' Processing helix chain 'A' and resid 920 through 929 removed outlier: 3.717A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.704A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 941 " --> pdb=" O PHE A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 990 removed outlier: 4.200A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1034 removed outlier: 3.727A pdb=" N ALA A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.539A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.691A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 519 removed outlier: 4.490A pdb=" N PHE B 517 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.710A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.583A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.528A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.904A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.611A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 814 removed outlier: 3.712A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.975A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.539A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.608A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.761A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.863A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.531A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.789A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.627A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.533A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.800A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.503A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 874 removed outlier: 3.797A pdb=" N GLN C 874 " --> pdb=" O PRO C 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 871 through 874' Processing helix chain 'C' and resid 920 through 929 removed outlier: 3.716A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.703A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 941 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 990 removed outlier: 4.199A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1034 removed outlier: 3.727A pdb=" N ALA C1010 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 470 removed outlier: 3.539A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.691A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 519 removed outlier: 4.491A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.710A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.584A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.528A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 665 through 677 removed outlier: 3.903A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.611A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 814 removed outlier: 3.712A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.386A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.408A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.408A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.694A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 876 through 880 removed outlier: 3.867A pdb=" N GLU A 877 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 868 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 866 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 396 removed outlier: 6.501A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.582A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.386A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.407A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.407A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.694A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 876 through 880 removed outlier: 3.867A pdb=" N GLU C 877 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 868 " --> pdb=" O GLU C 877 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 866 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AC2, first strand: chain 'D' and resid 394 through 396 removed outlier: 6.501A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.583A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2361 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: 5.42 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.17: 8 1.17 - 1.34: 4658 1.34 - 1.51: 5590 1.51 - 1.69: 6210 1.69 - 1.86: 190 Bond restraints: 16656 Sorted by residual: bond pdb=" C14 CLR A1107 " pdb=" C8 CLR A1107 " ideal model delta sigma weight residual 1.519 0.991 0.528 2.00e-02 2.50e+03 6.96e+02 bond pdb=" C14 CLR C1107 " pdb=" C8 CLR C1107 " ideal model delta sigma weight residual 1.519 0.993 0.526 2.00e-02 2.50e+03 6.90e+02 bond pdb=" C11 CLR A1107 " pdb=" C12 CLR A1107 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C11 CLR C1107 " pdb=" C12 CLR C1107 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C7 CLR C1107 " pdb=" C8 CLR C1107 " ideal model delta sigma weight residual 1.525 1.208 0.317 2.00e-02 2.50e+03 2.51e+02 ... (remaining 16651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.33: 22158 5.33 - 10.65: 241 10.65 - 15.98: 31 15.98 - 21.30: 3 21.30 - 26.63: 3 Bond angle restraints: 22436 Sorted by residual: angle pdb=" C12 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 111.01 84.38 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" C12 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C18 CLR C1107 " ideal model delta sigma weight residual 111.01 84.88 26.13 3.00e+00 1.11e-01 7.59e+01 angle pdb=" C14 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C18 CLR C1107 " ideal model delta sigma weight residual 112.24 90.51 21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C14 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 112.24 91.23 21.01 3.00e+00 1.11e-01 4.91e+01 angle pdb=" C12 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C17 CLR A1107 " ideal model delta sigma weight residual 116.52 133.32 -16.80 3.00e+00 1.11e-01 3.13e+01 ... (remaining 22431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9713 35.94 - 71.89: 258 71.89 - 107.83: 49 107.83 - 143.77: 5 143.77 - 179.71: 17 Dihedral angle restraints: 10042 sinusoidal: 4348 harmonic: 5694 Sorted by residual: dihedral pdb=" CA GLN C 508 " pdb=" C GLN C 508 " pdb=" N LYS C 509 " pdb=" CA LYS C 509 " ideal model delta harmonic sigma weight residual 180.00 142.34 37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA GLN A 508 " pdb=" C GLN A 508 " pdb=" N LYS A 509 " pdb=" CA LYS A 509 " ideal model delta harmonic sigma weight residual 180.00 142.46 37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA CYS A 589 " pdb=" C CYS A 589 " pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta harmonic sigma weight residual 180.00 145.43 34.57 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 10039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 2434 1.020 - 2.041: 2 2.041 - 3.061: 2 3.061 - 4.081: 0 4.081 - 5.102: 4 Chirality restraints: 2442 Sorted by residual: chirality pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C16 CLR A1107 " pdb=" C20 CLR A1107 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C17 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C16 CLR C1107 " pdb=" C20 CLR C1107 " both_signs ideal model delta sigma weight residual False 2.55 -2.51 5.06 2.00e-01 2.50e+01 6.40e+02 chirality pdb=" C9 CLR C1107 " pdb=" C10 CLR C1107 " pdb=" C11 CLR C1107 " pdb=" C8 CLR C1107 " both_signs ideal model delta sigma weight residual False -2.45 2.40 -4.84 2.00e-01 2.50e+01 5.87e+02 ... (remaining 2439 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 6ZP C1101 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.30e+01 pdb=" C03 6ZP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" C04 6ZP C1101 " 0.028 2.00e-02 2.50e+03 pdb=" C05 6ZP C1101 " 0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP C1101 " -0.031 2.00e-02 2.50e+03 pdb=" C07 6ZP C1101 " -0.023 2.00e-02 2.50e+03 pdb=" C08 6ZP C1101 " -0.004 2.00e-02 2.50e+03 pdb=" C09 6ZP C1101 " 0.025 2.00e-02 2.50e+03 pdb=" N01 6ZP C1101 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP A1101 " -0.035 2.00e-02 2.50e+03 3.08e-02 2.14e+01 pdb=" C03 6ZP A1101 " -0.028 2.00e-02 2.50e+03 pdb=" C04 6ZP A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C05 6ZP A1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP A1101 " 0.030 2.00e-02 2.50e+03 pdb=" C07 6ZP A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C08 6ZP A1101 " 0.004 2.00e-02 2.50e+03 pdb=" C09 6ZP A1101 " -0.025 2.00e-02 2.50e+03 pdb=" N01 6ZP A1101 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP B1101 " -0.022 2.00e-02 2.50e+03 1.81e-02 7.36e+00 pdb=" C03 6ZP B1101 " -0.016 2.00e-02 2.50e+03 pdb=" C04 6ZP B1101 " -0.013 2.00e-02 2.50e+03 pdb=" C05 6ZP B1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP B1101 " 0.019 2.00e-02 2.50e+03 pdb=" C07 6ZP B1101 " 0.014 2.00e-02 2.50e+03 pdb=" C08 6ZP B1101 " -0.006 2.00e-02 2.50e+03 pdb=" C09 6ZP B1101 " -0.011 2.00e-02 2.50e+03 pdb=" N01 6ZP B1101 " 0.037 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5060 2.84 - 3.36: 14584 3.36 - 3.87: 26916 3.87 - 4.39: 32360 4.39 - 4.90: 54069 Nonbonded interactions: 132989 Sorted by model distance: nonbonded pdb=" OH TYR D 533 " pdb=" O LEU D 577 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 533 " pdb=" O LEU B 577 " model vdw 2.329 3.040 nonbonded pdb=" OE1 GLN A 586 " pdb=" O HOH A1201 " model vdw 2.353 3.040 nonbonded pdb=" OE1 GLN C 586 " pdb=" O HOH C1201 " model vdw 2.355 3.040 nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D1201 " model vdw 2.359 3.040 ... (remaining 132984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 392 through 1034 or resid 1101 through 1107)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 392 through 817 or resid 1101 through 1105)) selection = chain 'D' } 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: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.014 0.528 16662 Z= 0.711 Angle : 1.360 26.627 22448 Z= 0.647 Chirality : 0.232 5.102 2442 Planarity : 0.007 0.063 2694 Dihedral : 17.975 179.713 6392 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.89 % Favored : 95.80 % Rotamer: Outliers : 0.36 % Allowed : 4.77 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.13), residues: 1954 helix: -3.58 (0.09), residues: 1078 sheet: -2.07 (0.32), residues: 182 loop : -2.68 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 861 HIS 0.003 0.001 HIS C 883 PHE 0.019 0.002 PHE D 667 TYR 0.030 0.002 TYR D 702 ARG 0.009 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.28239 ( 807) hydrogen bonds : angle 9.19478 ( 2361) SS BOND : bond 0.00308 ( 6) SS BOND : angle 0.92384 ( 12) covalent geometry : bond 0.01428 (16656) covalent geometry : angle 1.35973 (22436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 1.614 Fit side-chains REVERT: A 697 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7773 (mptt) REVERT: B 594 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5361 (mmm-85) REVERT: B 708 MET cc_start: 0.7829 (mmp) cc_final: 0.7497 (mmm) REVERT: C 435 HIS cc_start: 0.7645 (m90) cc_final: 0.7261 (t70) REVERT: C 569 ASN cc_start: 0.2051 (OUTLIER) cc_final: 0.1831 (t0) REVERT: C 594 ARG cc_start: 0.5929 (tpt-90) cc_final: 0.4611 (tmm160) REVERT: C 637 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6691 (mt-10) REVERT: C 865 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6135 (mt-10) REVERT: D 431 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 585 MET cc_start: 0.5263 (mpt) cc_final: 0.4956 (mmt) REVERT: D 663 LYS cc_start: 0.7610 (mttp) cc_final: 0.7357 (mttp) REVERT: D 708 MET cc_start: 0.7775 (mmp) cc_final: 0.7435 (mmm) outliers start: 6 outliers final: 0 residues processed: 329 average time/residue: 1.3666 time to fit residues: 494.0428 Evaluate side-chains 194 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN A 587 GLN A 726 ASN A 747 ASN A 947 ASN A 990 ASN B 747 ASN B 756 GLN C 412 HIS C 587 GLN C 726 ASN C 747 ASN C 947 ASN C 990 ASN D 587 GLN D 756 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.188530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148254 restraints weight = 18646.861| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.58 r_work: 0.3335 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16662 Z= 0.159 Angle : 0.864 35.107 22448 Z= 0.385 Chirality : 0.062 1.564 2442 Planarity : 0.005 0.056 2694 Dihedral : 19.943 178.325 2802 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 2.62 % Allowed : 11.26 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 1954 helix: -0.39 (0.14), residues: 1074 sheet: -1.76 (0.34), residues: 186 loop : -2.22 (0.20), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 766 HIS 0.009 0.002 HIS C 412 PHE 0.014 0.002 PHE B 579 TYR 0.019 0.002 TYR A 469 ARG 0.006 0.001 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 807) hydrogen bonds : angle 4.35393 ( 2361) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.53902 ( 12) covalent geometry : bond 0.00364 (16656) covalent geometry : angle 0.86428 (22436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8088 (mmm) cc_final: 0.7619 (mmm) REVERT: A 697 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7990 (mptt) REVERT: A 924 MET cc_start: 0.4677 (mmm) cc_final: 0.4372 (mmm) REVERT: A 966 PHE cc_start: 0.7145 (m-80) cc_final: 0.6843 (m-80) REVERT: B 427 ASP cc_start: 0.8494 (m-30) cc_final: 0.8145 (m-30) REVERT: B 435 HIS cc_start: 0.8036 (m-70) cc_final: 0.6680 (t-90) REVERT: C 393 LYS cc_start: 0.7664 (mtmt) cc_final: 0.7107 (mttt) REVERT: C 435 HIS cc_start: 0.7995 (m90) cc_final: 0.7470 (t70) REVERT: C 594 ARG cc_start: 0.6332 (tpt-90) cc_final: 0.5074 (tmm160) REVERT: C 738 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7881 (tttp) REVERT: C 865 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6559 (mt-10) REVERT: C 880 MET cc_start: 0.5657 (ptp) cc_final: 0.5422 (ptt) REVERT: C 924 MET cc_start: 0.6504 (mmt) cc_final: 0.5975 (mmm) REVERT: C 1031 ARG cc_start: 0.5713 (mmt180) cc_final: 0.5444 (ttm170) REVERT: D 397 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7983 (t) REVERT: D 435 HIS cc_start: 0.7970 (m-70) cc_final: 0.6680 (t-90) REVERT: D 587 GLN cc_start: 0.6673 (mm-40) cc_final: 0.5872 (mp10) outliers start: 44 outliers final: 14 residues processed: 251 average time/residue: 1.1681 time to fit residues: 327.6642 Evaluate side-chains 206 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 191 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 107 optimal weight: 0.0570 chunk 165 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS C 412 HIS C 586 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143231 restraints weight = 17784.854| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.91 r_work: 0.3231 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16662 Z= 0.115 Angle : 0.760 34.420 22448 Z= 0.334 Chirality : 0.061 1.584 2442 Planarity : 0.004 0.058 2694 Dihedral : 19.094 179.488 2800 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.38 % Allowed : 13.53 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1954 helix: 1.17 (0.16), residues: 1060 sheet: -1.58 (0.34), residues: 198 loop : -1.89 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.024 0.002 HIS A 412 PHE 0.020 0.001 PHE C 541 TYR 0.019 0.001 TYR A1001 ARG 0.007 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 807) hydrogen bonds : angle 3.85787 ( 2361) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.37922 ( 12) covalent geometry : bond 0.00252 (16656) covalent geometry : angle 0.75981 (22436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8392 (mmm) cc_final: 0.7985 (mmm) REVERT: A 435 HIS cc_start: 0.8297 (m90) cc_final: 0.7553 (t70) REVERT: A 697 LYS cc_start: 0.8446 (mtmm) cc_final: 0.7982 (mptt) REVERT: A 966 PHE cc_start: 0.6841 (m-80) cc_final: 0.6562 (m-80) REVERT: B 435 HIS cc_start: 0.8060 (m-70) cc_final: 0.6546 (t-90) REVERT: B 594 ARG cc_start: 0.6589 (mtt90) cc_final: 0.6183 (mmt90) REVERT: B 708 MET cc_start: 0.8736 (mmp) cc_final: 0.8465 (mmm) REVERT: C 393 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7104 (mttt) REVERT: C 435 HIS cc_start: 0.8245 (m90) cc_final: 0.7390 (t70) REVERT: C 447 ASP cc_start: 0.7737 (m-30) cc_final: 0.7473 (m-30) REVERT: C 785 SER cc_start: 0.6816 (m) cc_final: 0.6563 (p) REVERT: C 865 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6444 (mt-10) REVERT: C 884 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.6955 (m) REVERT: C 924 MET cc_start: 0.6480 (mmt) cc_final: 0.6109 (mmm) REVERT: D 435 HIS cc_start: 0.8011 (m-70) cc_final: 0.6517 (t-90) REVERT: D 587 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6014 (mp10) REVERT: D 599 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.4914 (mmt-90) outliers start: 40 outliers final: 15 residues processed: 221 average time/residue: 1.1592 time to fit residues: 286.8254 Evaluate side-chains 194 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 160 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 883 HIS C 412 HIS C 587 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135612 restraints weight = 17848.594| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.96 r_work: 0.3134 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16662 Z= 0.252 Angle : 0.863 34.948 22448 Z= 0.390 Chirality : 0.064 1.551 2442 Planarity : 0.005 0.065 2694 Dihedral : 19.065 177.900 2800 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.34 % Allowed : 13.77 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 1954 helix: 1.11 (0.15), residues: 1074 sheet: -1.61 (0.33), residues: 198 loop : -2.03 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 578 HIS 0.014 0.002 HIS A 412 PHE 0.020 0.002 PHE A 960 TYR 0.021 0.002 TYR A 469 ARG 0.006 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 807) hydrogen bonds : angle 4.03173 ( 2361) SS BOND : bond 0.00407 ( 6) SS BOND : angle 0.72897 ( 12) covalent geometry : bond 0.00617 (16656) covalent geometry : angle 0.86263 (22436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 1.631 Fit side-chains REVERT: A 408 MET cc_start: 0.8443 (mmm) cc_final: 0.7984 (mmm) REVERT: A 435 HIS cc_start: 0.8184 (m90) cc_final: 0.7310 (t70) REVERT: A 458 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7674 (mmtp) REVERT: A 594 ARG cc_start: 0.6881 (tpt-90) cc_final: 0.5691 (ttp-170) REVERT: A 684 ARG cc_start: 0.8254 (ptp90) cc_final: 0.7632 (ptm160) REVERT: A 966 PHE cc_start: 0.6911 (m-80) cc_final: 0.6707 (m-80) REVERT: A 1002 LYS cc_start: 0.6525 (tppp) cc_final: 0.5902 (tttp) REVERT: B 594 ARG cc_start: 0.6625 (mtt90) cc_final: 0.5594 (mmm160) REVERT: B 764 ASN cc_start: 0.8930 (m110) cc_final: 0.8725 (m-40) REVERT: C 435 HIS cc_start: 0.8271 (m90) cc_final: 0.7290 (t70) REVERT: C 486 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: C 509 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.5865 (tttm) REVERT: C 594 ARG cc_start: 0.6855 (tpt-90) cc_final: 0.5432 (tmm160) REVERT: C 834 ARG cc_start: 0.6486 (ptm160) cc_final: 0.5862 (mtm180) REVERT: C 865 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6465 (mt-10) REVERT: C 884 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.7052 (m) REVERT: C 924 MET cc_start: 0.6488 (mmt) cc_final: 0.6106 (mmm) REVERT: C 1002 LYS cc_start: 0.6625 (tppp) cc_final: 0.6114 (tttp) REVERT: D 435 HIS cc_start: 0.8110 (m-70) cc_final: 0.6397 (t-90) REVERT: D 587 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6423 (mp10) REVERT: D 594 ARG cc_start: 0.6835 (mtt90) cc_final: 0.5428 (mmm-85) REVERT: D 764 ASN cc_start: 0.8933 (m110) cc_final: 0.8732 (m-40) outliers start: 56 outliers final: 20 residues processed: 232 average time/residue: 1.2633 time to fit residues: 324.9889 Evaluate side-chains 196 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 741 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 125 optimal weight: 0.0270 chunk 115 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN C 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138445 restraints weight = 18071.825| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.84 r_work: 0.3165 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16662 Z= 0.133 Angle : 0.758 34.403 22448 Z= 0.334 Chirality : 0.061 1.591 2442 Planarity : 0.004 0.058 2694 Dihedral : 18.769 179.129 2800 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.40 % Allowed : 14.42 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1954 helix: 1.70 (0.16), residues: 1066 sheet: -1.54 (0.33), residues: 200 loop : -1.75 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1005 HIS 0.010 0.001 HIS A 412 PHE 0.023 0.001 PHE A 960 TYR 0.029 0.001 TYR A1032 ARG 0.007 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 807) hydrogen bonds : angle 3.74933 ( 2361) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.44706 ( 12) covalent geometry : bond 0.00314 (16656) covalent geometry : angle 0.75811 (22436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 1.548 Fit side-chains REVERT: A 392 GLN cc_start: 0.5275 (OUTLIER) cc_final: 0.5050 (pp30) REVERT: A 408 MET cc_start: 0.8357 (mmm) cc_final: 0.7891 (mmm) REVERT: A 435 HIS cc_start: 0.8091 (m90) cc_final: 0.7425 (t70) REVERT: A 684 ARG cc_start: 0.8111 (ptp90) cc_final: 0.7717 (ptm160) REVERT: A 697 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8092 (mptt) REVERT: A 952 ARG cc_start: 0.5079 (mtp180) cc_final: 0.4777 (tmm160) REVERT: A 1002 LYS cc_start: 0.6445 (tppp) cc_final: 0.5828 (tttp) REVERT: B 594 ARG cc_start: 0.6717 (mtt90) cc_final: 0.5545 (mmm-85) REVERT: C 393 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7290 (mttt) REVERT: C 411 ASN cc_start: 0.6698 (p0) cc_final: 0.6315 (p0) REVERT: C 414 MET cc_start: 0.6302 (mtm) cc_final: 0.6055 (ttm) REVERT: C 435 HIS cc_start: 0.8151 (m90) cc_final: 0.7399 (t70) REVERT: C 486 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: C 509 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.5682 (tttm) REVERT: C 591 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5288 (mp) REVERT: C 834 ARG cc_start: 0.6179 (ptm160) cc_final: 0.5963 (mtm180) REVERT: C 884 SER cc_start: 0.7438 (OUTLIER) cc_final: 0.7122 (m) REVERT: C 924 MET cc_start: 0.6373 (mmt) cc_final: 0.6014 (mmm) REVERT: C 1002 LYS cc_start: 0.6418 (tppp) cc_final: 0.5917 (tttp) REVERT: D 435 HIS cc_start: 0.7993 (m-70) cc_final: 0.6510 (t-90) REVERT: D 587 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6590 (mp10) REVERT: D 594 ARG cc_start: 0.6735 (mtt90) cc_final: 0.5465 (mmm-85) REVERT: D 599 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.5162 (mmt-90) outliers start: 57 outliers final: 26 residues processed: 219 average time/residue: 1.2287 time to fit residues: 299.2344 Evaluate side-chains 203 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 68 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 148 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.182860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138274 restraints weight = 17740.167| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.82 r_work: 0.3167 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16662 Z= 0.138 Angle : 0.754 34.066 22448 Z= 0.332 Chirality : 0.062 1.619 2442 Planarity : 0.004 0.057 2694 Dihedral : 18.598 179.932 2800 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.22 % Allowed : 14.66 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1954 helix: 1.85 (0.16), residues: 1070 sheet: -1.38 (0.34), residues: 196 loop : -1.70 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 766 HIS 0.010 0.001 HIS C 412 PHE 0.025 0.001 PHE A 960 TYR 0.022 0.001 TYR A1001 ARG 0.008 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 807) hydrogen bonds : angle 3.70966 ( 2361) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.41681 ( 12) covalent geometry : bond 0.00327 (16656) covalent geometry : angle 0.75441 (22436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 1.678 Fit side-chains REVERT: A 392 GLN cc_start: 0.5189 (OUTLIER) cc_final: 0.4981 (pp30) REVERT: A 408 MET cc_start: 0.8315 (mmm) cc_final: 0.7860 (mmm) REVERT: A 435 HIS cc_start: 0.8111 (m90) cc_final: 0.7411 (t70) REVERT: A 684 ARG cc_start: 0.8087 (ptp90) cc_final: 0.7645 (ptm160) REVERT: A 952 ARG cc_start: 0.5044 (mtp180) cc_final: 0.4729 (tmm160) REVERT: A 1002 LYS cc_start: 0.6532 (tppp) cc_final: 0.5812 (tttp) REVERT: B 594 ARG cc_start: 0.6833 (mtt90) cc_final: 0.5633 (mmm-85) REVERT: C 393 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7428 (mttt) REVERT: C 411 ASN cc_start: 0.6723 (p0) cc_final: 0.6386 (p0) REVERT: C 435 HIS cc_start: 0.8105 (m90) cc_final: 0.7293 (t70) REVERT: C 486 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: C 509 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5780 (tttm) REVERT: C 524 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: C 591 ILE cc_start: 0.5260 (OUTLIER) cc_final: 0.5017 (mp) REVERT: C 884 SER cc_start: 0.7271 (OUTLIER) cc_final: 0.6983 (m) REVERT: C 924 MET cc_start: 0.6423 (mmt) cc_final: 0.6149 (mmm) REVERT: C 1002 LYS cc_start: 0.6541 (tppp) cc_final: 0.5987 (tttp) REVERT: D 587 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6586 (mp10) REVERT: D 594 ARG cc_start: 0.6794 (mtt90) cc_final: 0.5506 (mmm-85) REVERT: D 599 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.5060 (mmt-90) outliers start: 54 outliers final: 25 residues processed: 214 average time/residue: 1.2543 time to fit residues: 298.6034 Evaluate side-chains 201 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 15 optimal weight: 0.0370 chunk 172 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 108 optimal weight: 0.0060 chunk 1 optimal weight: 0.0770 chunk 53 optimal weight: 5.9990 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141010 restraints weight = 17851.877| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.00 r_work: 0.3211 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16662 Z= 0.095 Angle : 0.712 33.452 22448 Z= 0.307 Chirality : 0.062 1.658 2442 Planarity : 0.004 0.053 2694 Dihedral : 18.248 179.822 2800 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.44 % Allowed : 16.21 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1954 helix: 2.25 (0.16), residues: 1070 sheet: -1.25 (0.36), residues: 188 loop : -1.53 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1005 HIS 0.010 0.001 HIS C 412 PHE 0.024 0.001 PHE A 960 TYR 0.023 0.001 TYR A1001 ARG 0.005 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 807) hydrogen bonds : angle 3.52139 ( 2361) SS BOND : bond 0.00063 ( 6) SS BOND : angle 0.48629 ( 12) covalent geometry : bond 0.00205 (16656) covalent geometry : angle 0.71242 (22436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 GLN cc_start: 0.5170 (OUTLIER) cc_final: 0.4947 (pp30) REVERT: A 408 MET cc_start: 0.8245 (mmm) cc_final: 0.7779 (mmm) REVERT: A 435 HIS cc_start: 0.8059 (m90) cc_final: 0.7356 (t70) REVERT: A 571 PHE cc_start: 0.5717 (m-10) cc_final: 0.5414 (m-80) REVERT: A 635 SER cc_start: 0.8588 (m) cc_final: 0.8362 (p) REVERT: A 684 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7592 (ptm160) REVERT: A 952 ARG cc_start: 0.5006 (mtp180) cc_final: 0.4766 (tmm160) REVERT: A 1002 LYS cc_start: 0.6431 (tppp) cc_final: 0.5747 (tttp) REVERT: B 594 ARG cc_start: 0.6739 (mtt90) cc_final: 0.5505 (mmm-85) REVERT: C 393 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7363 (mttt) REVERT: C 435 HIS cc_start: 0.8084 (m90) cc_final: 0.7356 (t-90) REVERT: C 486 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: C 509 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5866 (tttm) REVERT: C 524 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: C 579 PHE cc_start: 0.7930 (t80) cc_final: 0.7724 (t80) REVERT: C 635 SER cc_start: 0.8589 (m) cc_final: 0.8296 (p) REVERT: C 884 SER cc_start: 0.7079 (OUTLIER) cc_final: 0.6796 (m) REVERT: C 907 MET cc_start: 0.3267 (mmt) cc_final: 0.2169 (mtt) REVERT: C 924 MET cc_start: 0.6156 (mmt) cc_final: 0.5913 (mmm) REVERT: C 1002 LYS cc_start: 0.6298 (tppp) cc_final: 0.5801 (tttp) REVERT: D 435 HIS cc_start: 0.7824 (m-70) cc_final: 0.6343 (t-90) REVERT: D 457 THR cc_start: 0.8565 (p) cc_final: 0.8167 (p) REVERT: D 527 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6965 (mtt) REVERT: D 587 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6401 (mp10) outliers start: 41 outliers final: 20 residues processed: 217 average time/residue: 1.2832 time to fit residues: 309.1660 Evaluate side-chains 200 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 152 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 709 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 = 0.4105 r_free = 0.4105 target = 0.184405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139740 restraints weight = 17741.370| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.76 r_work: 0.3194 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16662 Z= 0.117 Angle : 0.728 33.456 22448 Z= 0.316 Chirality : 0.062 1.661 2442 Planarity : 0.004 0.053 2694 Dihedral : 18.172 179.893 2800 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.68 % Allowed : 16.75 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1954 helix: 2.26 (0.16), residues: 1070 sheet: -1.09 (0.36), residues: 198 loop : -1.52 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 606 HIS 0.009 0.001 HIS A 412 PHE 0.022 0.001 PHE A 960 TYR 0.025 0.001 TYR A1001 ARG 0.005 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 807) hydrogen bonds : angle 3.57374 ( 2361) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.48571 ( 12) covalent geometry : bond 0.00270 (16656) covalent geometry : angle 0.72796 (22436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 392 GLN cc_start: 0.5291 (OUTLIER) cc_final: 0.4990 (pp30) REVERT: A 408 MET cc_start: 0.8306 (mmm) cc_final: 0.7834 (mmm) REVERT: A 435 HIS cc_start: 0.8070 (m90) cc_final: 0.7387 (t-90) REVERT: A 571 PHE cc_start: 0.5492 (m-10) cc_final: 0.5283 (m-80) REVERT: A 635 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 684 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7619 (ptm160) REVERT: A 907 MET cc_start: 0.3456 (ttt) cc_final: 0.2821 (mpt) REVERT: A 952 ARG cc_start: 0.5026 (mtp180) cc_final: 0.4794 (tmm160) REVERT: A 1002 LYS cc_start: 0.6616 (tppp) cc_final: 0.5905 (tttp) REVERT: B 594 ARG cc_start: 0.6845 (mtt90) cc_final: 0.5630 (mmm-85) REVERT: C 393 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7260 (mttt) REVERT: C 435 HIS cc_start: 0.8086 (m90) cc_final: 0.7379 (t-90) REVERT: C 486 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7702 (mm-30) REVERT: C 509 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5840 (tttm) REVERT: C 524 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: C 635 SER cc_start: 0.8593 (m) cc_final: 0.8292 (p) REVERT: C 642 GLN cc_start: 0.7580 (pp30) cc_final: 0.7359 (pp30) REVERT: C 669 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7630 (ptmm) REVERT: C 884 SER cc_start: 0.7184 (OUTLIER) cc_final: 0.6913 (m) REVERT: C 907 MET cc_start: 0.3096 (mmt) cc_final: 0.2016 (mtt) REVERT: C 924 MET cc_start: 0.6174 (mmt) cc_final: 0.5960 (mmm) REVERT: C 1002 LYS cc_start: 0.6524 (tppp) cc_final: 0.5992 (tttp) REVERT: D 527 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7066 (mtt) REVERT: D 587 GLN cc_start: 0.6839 (mm-40) cc_final: 0.6501 (mp10) REVERT: D 594 ARG cc_start: 0.6810 (mtt90) cc_final: 0.5595 (mmm-85) outliers start: 45 outliers final: 23 residues processed: 206 average time/residue: 1.2892 time to fit residues: 293.6950 Evaluate side-chains 199 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 103 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 709 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 = 0.4116 r_free = 0.4116 target = 0.185388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140877 restraints weight = 17867.056| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.85 r_work: 0.3222 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16662 Z= 0.103 Angle : 0.718 33.254 22448 Z= 0.310 Chirality : 0.062 1.675 2442 Planarity : 0.004 0.055 2694 Dihedral : 18.004 179.606 2800 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.21 % Allowed : 17.16 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1954 helix: 2.37 (0.16), residues: 1070 sheet: -1.13 (0.36), residues: 188 loop : -1.43 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 606 HIS 0.009 0.001 HIS C 412 PHE 0.020 0.001 PHE A 960 TYR 0.023 0.001 TYR C1001 ARG 0.005 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 807) hydrogen bonds : angle 3.50983 ( 2361) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.34731 ( 12) covalent geometry : bond 0.00232 (16656) covalent geometry : angle 0.71829 (22436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8389 (mmm) cc_final: 0.7937 (mmm) REVERT: A 435 HIS cc_start: 0.8198 (m90) cc_final: 0.7341 (t-90) REVERT: A 635 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 684 ARG cc_start: 0.8244 (ptp90) cc_final: 0.7633 (ptm160) REVERT: A 907 MET cc_start: 0.3369 (ttt) cc_final: 0.2842 (mpt) REVERT: A 1002 LYS cc_start: 0.6607 (tppp) cc_final: 0.5888 (tttp) REVERT: B 594 ARG cc_start: 0.6844 (mtt90) cc_final: 0.5516 (mmm-85) REVERT: C 393 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7339 (mttt) REVERT: C 435 HIS cc_start: 0.8230 (m90) cc_final: 0.7339 (t-90) REVERT: C 486 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: C 509 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5926 (tttm) REVERT: C 524 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: C 635 SER cc_start: 0.8612 (m) cc_final: 0.8301 (p) REVERT: C 642 GLN cc_start: 0.7586 (pp30) cc_final: 0.7336 (pp30) REVERT: C 669 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7722 (ptmm) REVERT: C 738 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (tttp) REVERT: C 884 SER cc_start: 0.7059 (OUTLIER) cc_final: 0.6767 (m) REVERT: C 907 MET cc_start: 0.3177 (mmt) cc_final: 0.2059 (mtt) REVERT: C 1002 LYS cc_start: 0.6551 (tppp) cc_final: 0.5996 (tttp) REVERT: C 1029 MET cc_start: 0.5829 (mmm) cc_final: 0.5553 (mmm) REVERT: D 527 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7126 (mtt) REVERT: D 587 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6411 (mp10) REVERT: D 594 ARG cc_start: 0.6810 (mtt90) cc_final: 0.5524 (mmm-85) outliers start: 37 outliers final: 23 residues processed: 203 average time/residue: 1.2941 time to fit residues: 289.9632 Evaluate side-chains 199 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 709 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 = 0.4093 r_free = 0.4093 target = 0.183091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137750 restraints weight = 17877.946| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.94 r_work: 0.3171 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16662 Z= 0.154 Angle : 0.749 33.424 22448 Z= 0.329 Chirality : 0.063 1.669 2442 Planarity : 0.004 0.056 2694 Dihedral : 18.068 179.768 2800 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.03 % Allowed : 17.76 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1954 helix: 2.22 (0.16), residues: 1068 sheet: -1.01 (0.34), residues: 206 loop : -1.50 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 606 HIS 0.010 0.001 HIS A 412 PHE 0.021 0.001 PHE B 579 TYR 0.023 0.001 TYR C1001 ARG 0.004 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 807) hydrogen bonds : angle 3.62964 ( 2361) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.51852 ( 12) covalent geometry : bond 0.00373 (16656) covalent geometry : angle 0.74947 (22436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.877 Fit side-chains REVERT: A 408 MET cc_start: 0.8408 (mmm) cc_final: 0.7947 (mmm) REVERT: A 435 HIS cc_start: 0.8207 (m90) cc_final: 0.7343 (t-90) REVERT: A 629 MET cc_start: 0.8585 (tpp) cc_final: 0.8310 (mtt) REVERT: A 635 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 684 ARG cc_start: 0.8251 (ptp90) cc_final: 0.7681 (ptm160) REVERT: A 907 MET cc_start: 0.3433 (ttt) cc_final: 0.2871 (mpt) REVERT: A 1002 LYS cc_start: 0.6786 (tppp) cc_final: 0.6009 (tttp) REVERT: B 594 ARG cc_start: 0.6940 (mtt90) cc_final: 0.5681 (mmm-85) REVERT: C 435 HIS cc_start: 0.8262 (m90) cc_final: 0.7332 (t-90) REVERT: C 486 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: C 509 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5893 (tttm) REVERT: C 524 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: C 635 SER cc_start: 0.8677 (m) cc_final: 0.8334 (p) REVERT: C 642 GLN cc_start: 0.7648 (pp30) cc_final: 0.7362 (pp30) REVERT: C 669 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7698 (ptmm) REVERT: C 884 SER cc_start: 0.7207 (OUTLIER) cc_final: 0.6941 (m) REVERT: C 907 MET cc_start: 0.3227 (mmt) cc_final: 0.2085 (mtt) REVERT: C 985 ASN cc_start: 0.7494 (m110) cc_final: 0.7210 (m-40) REVERT: C 1002 LYS cc_start: 0.6486 (tppp) cc_final: 0.5915 (tttp) REVERT: C 1029 MET cc_start: 0.5873 (mmm) cc_final: 0.5598 (mmm) REVERT: D 587 GLN cc_start: 0.6844 (mm-40) cc_final: 0.6479 (mp10) REVERT: D 594 ARG cc_start: 0.6784 (mtt90) cc_final: 0.5662 (mmm-85) REVERT: D 599 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.5272 (mmt-90) outliers start: 34 outliers final: 23 residues processed: 200 average time/residue: 1.2735 time to fit residues: 283.3850 Evaluate side-chains 200 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 709 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 = 0.4080 r_free = 0.4080 target = 0.181762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136554 restraints weight = 17767.868| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.93 r_work: 0.3149 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16662 Z= 0.171 Angle : 0.768 33.472 22448 Z= 0.340 Chirality : 0.064 1.667 2442 Planarity : 0.004 0.058 2694 Dihedral : 18.142 179.872 2800 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.21 % Allowed : 17.64 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1954 helix: 2.03 (0.16), residues: 1068 sheet: -1.10 (0.34), residues: 206 loop : -1.57 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 606 HIS 0.010 0.002 HIS A 412 PHE 0.020 0.002 PHE B 579 TYR 0.025 0.002 TYR C1001 ARG 0.003 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 807) hydrogen bonds : angle 3.70951 ( 2361) SS BOND : bond 0.00330 ( 6) SS BOND : angle 0.65865 ( 12) covalent geometry : bond 0.00414 (16656) covalent geometry : angle 0.76844 (22436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12145.48 seconds wall clock time: 210 minutes 44.13 seconds (12644.13 seconds total)