Starting phenix.real_space_refine on Sun Aug 24 04:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss9_40748/08_2025/8ss9_40748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss9_40748/08_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_40748/08_2025/8ss9_40748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss9_40748/08_2025/8ss9_40748.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss9_40748/08_2025/8ss9_40748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss9_40748/08_2025/8ss9_40748.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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-4': 2, 'PCW:plan-2': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1} 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-2': 1, 'PCW:plan-1': 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-4': 2, 'PCW:plan-2': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1} 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-2': 1, 'PCW:plan-1': 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: 4.08, per 1000 atoms: 0.25 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: 1.44 Conformation dependent library (CDL) restraints added in 680.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.59 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: 2.75 Time building geometry restraints manager: 1.91 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 1107) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 392 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: 8.050 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.870 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.92 (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 ARG 0.009 0.001 ARG C 485 TYR 0.030 0.002 TYR D 702 PHE 0.019 0.002 PHE D 667 TRP 0.020 0.003 TRP A 861 HIS 0.003 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.01428 (16656) covalent geometry : angle 1.35973 (22436) SS BOND : bond 0.00308 ( 6) SS BOND : angle 0.92384 ( 12) hydrogen bonds : bond 0.28239 ( 807) hydrogen bonds : angle 9.19478 ( 2361) *********************** 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 : 0.604 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: 0.6670 time to fit residues: 240.6969 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 : 0.559 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 586 GLN C 726 ASN C 747 ASN C 947 ASN D 587 GLN D 756 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.186782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146847 restraints weight = 18512.504| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.69 r_work: 0.3299 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16662 Z= 0.195 Angle : 0.886 35.967 22448 Z= 0.397 Chirality : 0.059 1.373 2442 Planarity : 0.005 0.058 2694 Dihedral : 20.061 178.934 2802 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.21 % Rotamer: Outliers : 2.98 % Allowed : 11.03 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.17), residues: 1954 helix: -0.44 (0.14), residues: 1072 sheet: -1.77 (0.35), residues: 186 loop : -2.30 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 453 TYR 0.021 0.002 TYR A 469 PHE 0.016 0.002 PHE D 667 TRP 0.017 0.002 TRP A 766 HIS 0.010 0.002 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00443 (16656) covalent geometry : angle 0.88608 (22436) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.55666 ( 12) hydrogen bonds : bond 0.05165 ( 807) hydrogen bonds : angle 4.41064 ( 2361) *********************** 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 270 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8113 (mmm) cc_final: 0.7683 (mmm) REVERT: A 594 ARG cc_start: 0.6759 (tpt-90) cc_final: 0.5686 (ttp-170) REVERT: A 697 LYS cc_start: 0.8398 (mtmm) cc_final: 0.7992 (mptt) REVERT: A 907 MET cc_start: 0.4448 (ttm) cc_final: 0.4204 (ttt) REVERT: A 924 MET cc_start: 0.4690 (mmm) cc_final: 0.4380 (mmm) REVERT: A 966 PHE cc_start: 0.7131 (m-80) cc_final: 0.6861 (m-80) REVERT: B 399 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8411 (m) REVERT: B 435 HIS cc_start: 0.8098 (m-70) cc_final: 0.6703 (t-90) REVERT: C 393 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7085 (mttt) REVERT: C 408 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7609 (mmt) REVERT: C 435 HIS cc_start: 0.8030 (m90) cc_final: 0.7462 (t70) REVERT: C 594 ARG cc_start: 0.6408 (tpt-90) cc_final: 0.5129 (tmm160) REVERT: C 738 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7946 (tttp) REVERT: C 785 SER cc_start: 0.6796 (m) cc_final: 0.6495 (p) REVERT: C 865 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6625 (mt-10) REVERT: C 880 MET cc_start: 0.5637 (ptp) cc_final: 0.5397 (ptt) REVERT: C 924 MET cc_start: 0.6512 (mmt) cc_final: 0.5993 (mmm) REVERT: C 1031 ARG cc_start: 0.5821 (mmt180) cc_final: 0.5569 (ttm170) REVERT: D 397 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7951 (t) REVERT: D 435 HIS cc_start: 0.8023 (m-70) cc_final: 0.6670 (t-90) REVERT: D 442 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8200 (mp) REVERT: D 587 GLN cc_start: 0.6770 (mm-40) cc_final: 0.5999 (mp10) REVERT: D 719 ASP cc_start: 0.7187 (t0) cc_final: 0.6808 (t0) outliers start: 50 outliers final: 16 residues processed: 251 average time/residue: 0.6031 time to fit residues: 168.8340 Evaluate side-chains 214 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 486 GLU 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 884 SER Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR 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 408 MET 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 442 LEU Chi-restraints excluded: chain D residue 516 SER 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 23 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 175 optimal weight: 0.1980 chunk 179 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141126 restraints weight = 18030.570| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.77 r_work: 0.3205 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2918 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= 0.132 Angle : 0.775 34.750 22448 Z= 0.343 Chirality : 0.061 1.561 2442 Planarity : 0.004 0.060 2694 Dihedral : 19.172 178.962 2800 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.98 % Allowed : 12.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 1954 helix: 1.03 (0.16), residues: 1058 sheet: -1.62 (0.34), residues: 198 loop : -1.98 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 453 TYR 0.019 0.001 TYR A1001 PHE 0.021 0.001 PHE C 541 TRP 0.016 0.001 TRP A 766 HIS 0.020 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00300 (16656) covalent geometry : angle 0.77547 (22436) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.38922 ( 12) hydrogen bonds : bond 0.04184 ( 807) hydrogen bonds : angle 3.93518 ( 2361) *********************** 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 239 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.593 Fit side-chains REVERT: A 408 MET cc_start: 0.8373 (mmm) cc_final: 0.7905 (mmm) REVERT: A 435 HIS cc_start: 0.8065 (m90) cc_final: 0.7510 (t70) REVERT: A 594 ARG cc_start: 0.6865 (tpt-90) cc_final: 0.5743 (ttp-170) REVERT: A 697 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8082 (mptt) REVERT: A 966 PHE cc_start: 0.6907 (m-80) cc_final: 0.6619 (m-80) REVERT: A 1002 LYS cc_start: 0.6390 (tppp) cc_final: 0.5980 (tttp) REVERT: B 397 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7945 (t) REVERT: B 399 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 435 HIS cc_start: 0.7971 (m-70) cc_final: 0.6556 (t-90) REVERT: B 594 ARG cc_start: 0.6629 (mtt90) cc_final: 0.6241 (mmt90) REVERT: C 393 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7236 (mttt) REVERT: C 435 HIS cc_start: 0.8178 (m90) cc_final: 0.7505 (t70) REVERT: C 594 ARG cc_start: 0.6601 (tpt-90) cc_final: 0.5270 (tmm160) REVERT: C 865 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6431 (mt-10) REVERT: C 880 MET cc_start: 0.5676 (ptp) cc_final: 0.5373 (ptt) REVERT: C 924 MET cc_start: 0.6488 (mmt) cc_final: 0.6018 (mmm) REVERT: D 397 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.8013 (t) REVERT: D 435 HIS cc_start: 0.7924 (m-70) cc_final: 0.6510 (t-90) REVERT: D 587 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6157 (mp10) outliers start: 50 outliers final: 14 residues processed: 221 average time/residue: 0.5895 time to fit residues: 145.2528 Evaluate side-chains 195 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1032 TYR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR 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 498 LEU 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 1013 SER Chi-restraints excluded: chain D residue 397 VAL 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 46 optimal weight: 6.9990 chunk 170 optimal weight: 0.0870 chunk 194 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 = 0.183018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137318 restraints weight = 17832.576| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.89 r_work: 0.3164 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3347 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= 0.164 Angle : 0.788 34.650 22448 Z= 0.350 Chirality : 0.062 1.576 2442 Planarity : 0.004 0.059 2694 Dihedral : 18.902 178.172 2800 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.34 % Allowed : 14.18 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1954 helix: 1.42 (0.16), residues: 1076 sheet: -1.58 (0.34), residues: 198 loop : -1.91 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 453 TYR 0.019 0.002 TYR A1001 PHE 0.022 0.002 PHE A 960 TRP 0.014 0.002 TRP A 766 HIS 0.011 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00390 (16656) covalent geometry : angle 0.78837 (22436) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.46116 ( 12) hydrogen bonds : bond 0.04087 ( 807) hydrogen bonds : angle 3.83028 ( 2361) *********************** 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 242 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8449 (mmm) cc_final: 0.8010 (mmm) REVERT: A 435 HIS cc_start: 0.8234 (m90) cc_final: 0.7394 (t70) REVERT: A 684 ARG cc_start: 0.8212 (ptp90) cc_final: 0.7640 (ptm160) REVERT: A 697 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8088 (mptt) REVERT: A 966 PHE cc_start: 0.6808 (m-80) cc_final: 0.6581 (m-80) REVERT: A 1002 LYS cc_start: 0.6462 (tppp) cc_final: 0.5938 (tttp) REVERT: B 397 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7964 (t) REVERT: B 594 ARG cc_start: 0.6688 (mtt90) cc_final: 0.5386 (mmm-85) REVERT: B 764 ASN cc_start: 0.8917 (m110) cc_final: 0.8699 (m-40) REVERT: C 393 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7195 (mttt) REVERT: C 435 HIS cc_start: 0.8268 (m90) cc_final: 0.7300 (t70) REVERT: C 509 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.5708 (tttm) REVERT: C 834 ARG cc_start: 0.6462 (ptm160) cc_final: 0.5845 (mtm180) REVERT: C 865 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6396 (tt0) REVERT: C 884 SER cc_start: 0.7352 (OUTLIER) cc_final: 0.6966 (m) REVERT: C 924 MET cc_start: 0.6540 (mmt) cc_final: 0.6194 (mmm) REVERT: C 1002 LYS cc_start: 0.6327 (tppp) cc_final: 0.5921 (tttp) REVERT: D 397 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7988 (t) REVERT: D 435 HIS cc_start: 0.8052 (m-70) cc_final: 0.6436 (t-90) REVERT: D 587 GLN cc_start: 0.6726 (mm-40) cc_final: 0.6378 (mp10) outliers start: 56 outliers final: 24 residues processed: 225 average time/residue: 0.6356 time to fit residues: 158.6769 Evaluate side-chains 208 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 864 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 397 VAL 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 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL 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 C residue 1032 TYR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 31 optimal weight: 0.0670 chunk 96 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 109 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.183604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138941 restraints weight = 17875.202| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.76 r_work: 0.3182 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16662 Z= 0.131 Angle : 0.749 34.249 22448 Z= 0.330 Chirality : 0.062 1.604 2442 Planarity : 0.004 0.058 2694 Dihedral : 18.673 179.099 2800 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.46 % Allowed : 14.30 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 1954 helix: 1.86 (0.16), residues: 1066 sheet: -1.54 (0.34), residues: 200 loop : -1.69 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 453 TYR 0.021 0.001 TYR A1001 PHE 0.023 0.001 PHE A 960 TRP 0.013 0.002 TRP A1005 HIS 0.010 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00307 (16656) covalent geometry : angle 0.74904 (22436) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.43118 ( 12) hydrogen bonds : bond 0.03668 ( 807) hydrogen bonds : angle 3.69356 ( 2361) *********************** 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 237 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8337 (mmm) cc_final: 0.7890 (mmm) REVERT: A 435 HIS cc_start: 0.8109 (m90) cc_final: 0.7409 (t70) REVERT: A 684 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7618 (ptm160) REVERT: A 697 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8031 (mptt) REVERT: A 952 ARG cc_start: 0.5091 (mtp180) cc_final: 0.4775 (tmm160) REVERT: A 966 PHE cc_start: 0.6880 (m-80) cc_final: 0.6617 (m-80) REVERT: A 1002 LYS cc_start: 0.6379 (tppp) cc_final: 0.5827 (tttp) REVERT: B 397 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7998 (t) REVERT: B 594 ARG cc_start: 0.6748 (mtt90) cc_final: 0.5487 (mmm-85) REVERT: C 393 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7267 (mttt) REVERT: C 411 ASN cc_start: 0.6687 (p0) cc_final: 0.6342 (p0) REVERT: C 435 HIS cc_start: 0.8143 (m90) cc_final: 0.7373 (t70) REVERT: C 509 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5720 (tttm) REVERT: C 738 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8004 (tttp) REVERT: C 834 ARG cc_start: 0.6134 (ptm160) cc_final: 0.5913 (mtm180) REVERT: C 865 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6289 (tt0) REVERT: C 884 SER cc_start: 0.7271 (OUTLIER) cc_final: 0.6956 (m) REVERT: C 924 MET cc_start: 0.6327 (mmt) cc_final: 0.6025 (mmm) REVERT: C 1002 LYS cc_start: 0.6349 (tppp) cc_final: 0.5887 (tttp) REVERT: D 397 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7979 (t) REVERT: D 435 HIS cc_start: 0.7954 (m-70) cc_final: 0.6437 (t-90) REVERT: D 527 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7096 (mtt) REVERT: D 587 GLN cc_start: 0.6779 (mm-40) cc_final: 0.6522 (mp10) REVERT: D 599 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.5223 (mmt-90) outliers start: 58 outliers final: 28 residues processed: 222 average time/residue: 0.6557 time to fit residues: 161.5945 Evaluate side-chains 208 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN 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 936 LEU Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 442 LEU 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 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 738 LYS 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 397 VAL Chi-restraints excluded: chain D residue 442 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN A 587 GLN C 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.181785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137365 restraints weight = 17859.432| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.86 r_work: 0.3139 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3720 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= 0.174 Angle : 0.781 34.215 22448 Z= 0.347 Chirality : 0.063 1.609 2442 Planarity : 0.004 0.059 2694 Dihedral : 18.643 179.761 2800 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.64 % Allowed : 14.42 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.19), residues: 1954 helix: 1.69 (0.16), residues: 1080 sheet: -1.42 (0.34), residues: 196 loop : -1.81 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 453 TYR 0.030 0.002 TYR C1032 PHE 0.025 0.002 PHE A 960 TRP 0.013 0.002 TRP A 766 HIS 0.011 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00419 (16656) covalent geometry : angle 0.78105 (22436) SS BOND : bond 0.00331 ( 6) SS BOND : angle 0.56553 ( 12) hydrogen bonds : bond 0.03903 ( 807) hydrogen bonds : angle 3.76487 ( 2361) *********************** 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 236 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.510 Fit side-chains REVERT: A 408 MET cc_start: 0.8347 (mmm) cc_final: 0.7882 (mmm) REVERT: A 435 HIS cc_start: 0.8090 (m90) cc_final: 0.7344 (t70) REVERT: A 684 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7619 (ptm160) REVERT: A 952 ARG cc_start: 0.4995 (mtp180) cc_final: 0.4712 (tmm160) REVERT: A 1002 LYS cc_start: 0.6560 (tppp) cc_final: 0.5850 (tttp) REVERT: B 397 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7914 (t) REVERT: B 587 GLN cc_start: 0.5829 (OUTLIER) cc_final: 0.4598 (mp10) REVERT: B 594 ARG cc_start: 0.6861 (mtt90) cc_final: 0.5681 (mmm-85) REVERT: B 764 ASN cc_start: 0.8797 (m110) cc_final: 0.8594 (m-40) REVERT: C 393 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7389 (mttt) REVERT: C 411 ASN cc_start: 0.6747 (p0) cc_final: 0.6414 (p0) REVERT: C 435 HIS cc_start: 0.8104 (m90) cc_final: 0.7279 (t70) REVERT: C 509 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5756 (tttm) REVERT: C 629 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8366 (mtt) REVERT: C 884 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7090 (m) REVERT: C 924 MET cc_start: 0.6399 (mmt) cc_final: 0.6092 (mmm) REVERT: C 1002 LYS cc_start: 0.6531 (tppp) cc_final: 0.5992 (tttp) REVERT: D 397 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7925 (t) REVERT: D 587 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6595 (mp10) REVERT: D 594 ARG cc_start: 0.6858 (mtt90) cc_final: 0.5516 (mmm-85) REVERT: D 599 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5217 (mmt-90) outliers start: 61 outliers final: 28 residues processed: 220 average time/residue: 0.6379 time to fit residues: 155.3954 Evaluate side-chains 207 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN 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 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 LYS 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 543 VAL Chi-restraints excluded: chain C residue 629 MET 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 397 VAL 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 162 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 chunk 94 optimal weight: 0.0270 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.182258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137216 restraints weight = 17734.980| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.68 r_work: 0.3161 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16662 Z= 0.150 Angle : 0.755 33.840 22448 Z= 0.333 Chirality : 0.063 1.635 2442 Planarity : 0.004 0.057 2694 Dihedral : 18.500 178.935 2800 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.22 % Allowed : 15.26 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.19), residues: 1954 helix: 1.91 (0.16), residues: 1068 sheet: -1.32 (0.35), residues: 196 loop : -1.73 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 453 TYR 0.023 0.001 TYR A1001 PHE 0.026 0.002 PHE A 960 TRP 0.013 0.002 TRP C 766 HIS 0.010 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00358 (16656) covalent geometry : angle 0.75532 (22436) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.47481 ( 12) hydrogen bonds : bond 0.03703 ( 807) hydrogen bonds : angle 3.68129 ( 2361) *********************** 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 233 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.494 Fit side-chains REVERT: A 408 MET cc_start: 0.8409 (mmm) cc_final: 0.7953 (mmm) REVERT: A 435 HIS cc_start: 0.8224 (m90) cc_final: 0.7273 (t70) REVERT: A 511 LYS cc_start: 0.7322 (tttm) cc_final: 0.7070 (tppt) REVERT: A 571 PHE cc_start: 0.5794 (m-10) cc_final: 0.5496 (m-80) REVERT: A 684 ARG cc_start: 0.8278 (ptp90) cc_final: 0.7687 (ptm160) REVERT: A 952 ARG cc_start: 0.4975 (mtp180) cc_final: 0.4706 (tmm160) REVERT: A 1002 LYS cc_start: 0.6730 (tppp) cc_final: 0.5920 (tttp) REVERT: A 1023 MET cc_start: 0.6071 (mmt) cc_final: 0.5865 (mmm) REVERT: B 397 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7918 (t) REVERT: B 594 ARG cc_start: 0.6906 (mtt90) cc_final: 0.5633 (mmm-85) REVERT: B 764 ASN cc_start: 0.8911 (m110) cc_final: 0.8695 (m-40) REVERT: C 393 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7391 (mttt) REVERT: C 435 HIS cc_start: 0.8217 (m90) cc_final: 0.7241 (t-90) REVERT: C 509 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5735 (tttm) REVERT: C 524 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: C 579 PHE cc_start: 0.7984 (t80) cc_final: 0.7696 (t80) REVERT: C 629 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: C 884 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7067 (m) REVERT: C 924 MET cc_start: 0.6319 (mmt) cc_final: 0.6058 (mmm) REVERT: C 1002 LYS cc_start: 0.6616 (tppp) cc_final: 0.5985 (tttp) REVERT: D 397 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7937 (t) REVERT: D 587 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6625 (mp10) REVERT: D 594 ARG cc_start: 0.6877 (mtt90) cc_final: 0.5648 (mmm-85) REVERT: D 599 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.5324 (mmt-90) outliers start: 54 outliers final: 29 residues processed: 218 average time/residue: 0.5399 time to fit residues: 130.4445 Evaluate side-chains 209 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 397 VAL 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 772 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 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 629 MET 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 C residue 1032 TYR Chi-restraints excluded: chain D residue 397 VAL 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 699 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.182452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136267 restraints weight = 18011.258| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.94 r_work: 0.3168 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16662 Z= 0.130 Angle : 0.740 33.536 22448 Z= 0.323 Chirality : 0.063 1.654 2442 Planarity : 0.004 0.055 2694 Dihedral : 18.314 179.650 2800 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.16 % Allowed : 15.67 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1954 helix: 2.04 (0.16), residues: 1070 sheet: -1.09 (0.34), residues: 206 loop : -1.61 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 453 TYR 0.025 0.001 TYR C1001 PHE 0.026 0.001 PHE A 960 TRP 0.013 0.002 TRP A 606 HIS 0.010 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00304 (16656) covalent geometry : angle 0.73986 (22436) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.38336 ( 12) hydrogen bonds : bond 0.03500 ( 807) hydrogen bonds : angle 3.62784 ( 2361) *********************** 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 227 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8364 (mmm) cc_final: 0.7899 (mmm) REVERT: A 435 HIS cc_start: 0.8267 (m90) cc_final: 0.7292 (t70) REVERT: A 571 PHE cc_start: 0.5402 (m-10) cc_final: 0.5140 (m-80) REVERT: A 635 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 684 ARG cc_start: 0.8195 (ptp90) cc_final: 0.7570 (ptm160) REVERT: A 952 ARG cc_start: 0.4924 (mtp180) cc_final: 0.4649 (tmm160) REVERT: A 1002 LYS cc_start: 0.6676 (tppp) cc_final: 0.5854 (tttp) REVERT: B 397 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7822 (t) REVERT: B 594 ARG cc_start: 0.6936 (mtt90) cc_final: 0.5570 (mmm-85) REVERT: B 764 ASN cc_start: 0.8844 (m110) cc_final: 0.8625 (m-40) REVERT: C 435 HIS cc_start: 0.8221 (m90) cc_final: 0.7199 (t-90) REVERT: C 509 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5831 (tttm) REVERT: C 524 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: C 579 PHE cc_start: 0.7868 (t80) cc_final: 0.7645 (t80) REVERT: C 629 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8297 (mtt) REVERT: C 635 SER cc_start: 0.8655 (m) cc_final: 0.8298 (p) REVERT: C 669 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7495 (ptmm) REVERT: C 884 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6862 (m) REVERT: C 907 MET cc_start: 0.3088 (mmt) cc_final: 0.2028 (mtt) REVERT: C 924 MET cc_start: 0.6267 (mmt) cc_final: 0.6007 (mmm) REVERT: C 1002 LYS cc_start: 0.6442 (tppp) cc_final: 0.5768 (tttp) REVERT: D 397 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7877 (t) REVERT: D 587 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6435 (mp10) REVERT: D 594 ARG cc_start: 0.6771 (mtt90) cc_final: 0.5439 (mmm-85) outliers start: 53 outliers final: 28 residues processed: 215 average time/residue: 0.5912 time to fit residues: 140.9861 Evaluate side-chains 208 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 397 VAL 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 772 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 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 629 MET 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 C residue 1032 TYR Chi-restraints excluded: chain D residue 397 VAL 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 741 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 190 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.182473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135834 restraints weight = 17994.149| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.97 r_work: 0.3177 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16662 Z= 0.128 Angle : 0.742 33.457 22448 Z= 0.325 Chirality : 0.063 1.662 2442 Planarity : 0.004 0.058 2694 Dihedral : 18.246 179.955 2800 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.74 % Allowed : 16.39 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.19), residues: 1954 helix: 2.10 (0.16), residues: 1070 sheet: -1.13 (0.35), residues: 196 loop : -1.56 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.029 0.001 TYR A1032 PHE 0.026 0.001 PHE A 960 TRP 0.016 0.002 TRP C 606 HIS 0.010 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00302 (16656) covalent geometry : angle 0.74258 (22436) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.36098 ( 12) hydrogen bonds : bond 0.03493 ( 807) hydrogen bonds : angle 3.62388 ( 2361) *********************** 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 222 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8355 (mmm) cc_final: 0.7893 (mmm) REVERT: A 435 HIS cc_start: 0.8271 (m90) cc_final: 0.7313 (t70) REVERT: A 571 PHE cc_start: 0.5304 (m-10) cc_final: 0.5027 (m-80) REVERT: A 635 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 684 ARG cc_start: 0.8201 (ptp90) cc_final: 0.7598 (ptm160) REVERT: A 952 ARG cc_start: 0.4979 (mtp180) cc_final: 0.4688 (tmm160) REVERT: A 1002 LYS cc_start: 0.6766 (tppp) cc_final: 0.5967 (tttp) REVERT: B 397 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7813 (t) REVERT: B 587 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.4571 (mp10) REVERT: B 594 ARG cc_start: 0.6934 (mtt90) cc_final: 0.5614 (mmm-85) REVERT: B 764 ASN cc_start: 0.8855 (m110) cc_final: 0.8639 (m-40) REVERT: C 435 HIS cc_start: 0.8228 (m90) cc_final: 0.7220 (t-90) REVERT: C 509 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5827 (tttm) REVERT: C 524 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: C 579 PHE cc_start: 0.7909 (t80) cc_final: 0.7660 (t80) REVERT: C 629 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: C 635 SER cc_start: 0.8639 (m) cc_final: 0.8294 (p) REVERT: C 669 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7612 (ptmm) REVERT: C 884 SER cc_start: 0.7132 (OUTLIER) cc_final: 0.6872 (m) REVERT: C 907 MET cc_start: 0.2972 (mmt) cc_final: 0.1953 (mtt) REVERT: C 985 ASN cc_start: 0.7436 (m110) cc_final: 0.7118 (m-40) REVERT: C 1002 LYS cc_start: 0.6442 (tppp) cc_final: 0.5778 (tttp) REVERT: D 397 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7887 (t) REVERT: D 587 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6530 (mp10) REVERT: D 594 ARG cc_start: 0.6772 (mtt90) cc_final: 0.5463 (mmm-85) outliers start: 46 outliers final: 29 residues processed: 211 average time/residue: 0.5434 time to fit residues: 126.6717 Evaluate side-chains 210 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 772 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 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 629 MET 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 C residue 1032 TYR Chi-restraints excluded: chain D residue 397 VAL 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 741 SER 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 143 optimal weight: 0.0010 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 197 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.183157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137679 restraints weight = 17909.008| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.01 r_work: 0.3194 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16662 Z= 0.117 Angle : 0.730 33.224 22448 Z= 0.318 Chirality : 0.063 1.674 2442 Planarity : 0.004 0.057 2694 Dihedral : 18.102 179.648 2800 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.38 % Allowed : 16.92 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.19), residues: 1954 helix: 2.21 (0.16), residues: 1070 sheet: -1.06 (0.36), residues: 196 loop : -1.51 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.026 0.001 TYR C1001 PHE 0.023 0.001 PHE A 960 TRP 0.021 0.002 TRP A 606 HIS 0.011 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00271 (16656) covalent geometry : angle 0.72971 (22436) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.31235 ( 12) hydrogen bonds : bond 0.03368 ( 807) hydrogen bonds : angle 3.58508 ( 2361) ********************** 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 214 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8334 (mmm) cc_final: 0.7874 (mmm) REVERT: A 435 HIS cc_start: 0.8240 (m90) cc_final: 0.7299 (t70) REVERT: A 571 PHE cc_start: 0.5204 (m-10) cc_final: 0.4969 (m-80) REVERT: A 635 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8367 (p) REVERT: A 669 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7687 (ptmm) REVERT: A 684 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7611 (ptm160) REVERT: A 907 MET cc_start: 0.3377 (ttt) cc_final: 0.2813 (mpt) REVERT: A 952 ARG cc_start: 0.4958 (mtp180) cc_final: 0.4685 (tmm160) REVERT: A 966 PHE cc_start: 0.6694 (m-80) cc_final: 0.6055 (m-80) REVERT: A 1002 LYS cc_start: 0.6752 (tppp) cc_final: 0.5981 (tttp) REVERT: B 594 ARG cc_start: 0.6940 (mtt90) cc_final: 0.5663 (mmm-85) REVERT: B 764 ASN cc_start: 0.8809 (m110) cc_final: 0.8592 (m-40) REVERT: C 435 HIS cc_start: 0.8248 (m90) cc_final: 0.7297 (t-90) REVERT: C 509 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5733 (tttm) REVERT: C 524 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: C 579 PHE cc_start: 0.7887 (t80) cc_final: 0.7636 (t80) REVERT: C 629 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8264 (mtt) REVERT: C 635 SER cc_start: 0.8614 (m) cc_final: 0.8287 (p) REVERT: C 669 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7755 (ptmm) REVERT: C 884 SER cc_start: 0.7062 (OUTLIER) cc_final: 0.6784 (m) REVERT: C 907 MET cc_start: 0.3086 (mmt) cc_final: 0.2005 (mtt) REVERT: C 985 ASN cc_start: 0.7444 (m110) cc_final: 0.7094 (m-40) REVERT: C 1002 LYS cc_start: 0.6439 (tppp) cc_final: 0.5770 (tttp) REVERT: C 1029 MET cc_start: 0.5738 (mmm) cc_final: 0.5494 (mmm) REVERT: D 397 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7876 (t) REVERT: D 587 GLN cc_start: 0.6872 (mm-40) cc_final: 0.6477 (mp10) REVERT: D 594 ARG cc_start: 0.6717 (mtt90) cc_final: 0.5452 (mmm-85) outliers start: 40 outliers final: 31 residues processed: 206 average time/residue: 0.5800 time to fit residues: 132.4396 Evaluate side-chains 208 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 884 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 393 LYS 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 772 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 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 629 MET 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 1001 TYR Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 397 VAL 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 699 LYS Chi-restraints excluded: chain D residue 741 SER 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 107 optimal weight: 0.0870 chunk 131 optimal weight: 0.5980 chunk 176 optimal weight: 0.0010 chunk 153 optimal weight: 0.0060 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4143 r_free = 0.4143 target = 0.186915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142098 restraints weight = 18197.949| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.69 r_work: 0.3268 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16662 Z= 0.092 Angle : 0.714 32.890 22448 Z= 0.305 Chirality : 0.062 1.691 2442 Planarity : 0.004 0.054 2694 Dihedral : 17.828 179.785 2800 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.09 % Allowed : 17.16 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.20), residues: 1954 helix: 2.48 (0.16), residues: 1066 sheet: -1.06 (0.36), residues: 188 loop : -1.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.026 0.001 TYR C1001 PHE 0.021 0.001 PHE A 579 TRP 0.018 0.001 TRP C 606 HIS 0.011 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00198 (16656) covalent geometry : angle 0.71442 (22436) SS BOND : bond 0.00069 ( 6) SS BOND : angle 0.37828 ( 12) hydrogen bonds : bond 0.02976 ( 807) hydrogen bonds : angle 3.45748 ( 2361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6157.59 seconds wall clock time: 105 minutes 35.33 seconds (6335.33 seconds total)