Starting phenix.real_space_refine on Mon Oct 14 06:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/10_2024/8ss9_40748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/10_2024/8ss9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/10_2024/8ss9_40748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/10_2024/8ss9_40748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/10_2024/8ss9_40748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/10_2024/8ss9_40748.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.179 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 14 5.49 5 S 104 5.16 5 Na 2 4.78 5 C 10718 2.51 5 N 2540 2.21 5 O 2929 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "C" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 230 Unusual residues: {' NA': 1, '6ZP': 1, 'CLR': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Unusual residues: {' NA': 1, '6ZP': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'6ZP': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 10.36, per 1000 atoms: 0.63 Number of scatterers: 16319 At special positions: 0 Unit cell: (117.475, 132.275, 134.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 104 16.00 P 14 15.00 Na 2 11.00 F 12 9.00 O 2929 8.00 N 2540 7.00 C 10718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 56.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.975A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.539A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.608A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.761A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.863A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.532A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.789A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.627A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.534A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.800A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.503A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 874 removed outlier: 3.797A pdb=" N GLN A 874 " --> pdb=" O PRO A 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 871 through 874' Processing helix chain 'A' and resid 920 through 929 removed outlier: 3.717A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.704A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 941 " --> pdb=" O PHE A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 990 removed outlier: 4.200A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1034 removed outlier: 3.727A pdb=" N ALA A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.539A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.691A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 519 removed outlier: 4.490A pdb=" N PHE B 517 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.710A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.583A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.528A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.904A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.611A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 814 removed outlier: 3.712A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.975A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.539A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.608A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.761A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.863A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.531A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.789A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.627A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.533A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.800A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.503A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 874 removed outlier: 3.797A pdb=" N GLN C 874 " --> pdb=" O PRO C 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 871 through 874' Processing helix chain 'C' and resid 920 through 929 removed outlier: 3.716A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.703A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 941 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 990 removed outlier: 4.199A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1034 removed outlier: 3.727A pdb=" N ALA C1010 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 470 removed outlier: 3.539A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.691A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 519 removed outlier: 4.491A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.710A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.584A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.528A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 665 through 677 removed outlier: 3.903A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.611A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 814 removed outlier: 3.712A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.386A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.408A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.408A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.694A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 876 through 880 removed outlier: 3.867A pdb=" N GLU A 877 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 868 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 866 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 396 removed outlier: 6.501A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.582A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.386A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.407A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.407A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.694A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 876 through 880 removed outlier: 3.867A pdb=" N GLU C 877 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 868 " --> pdb=" O GLU C 877 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 866 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AC2, first strand: chain 'D' and resid 394 through 396 removed outlier: 6.501A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.805A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.583A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.17: 8 1.17 - 1.34: 4658 1.34 - 1.51: 5590 1.51 - 1.69: 6210 1.69 - 1.86: 190 Bond restraints: 16656 Sorted by residual: bond pdb=" C14 CLR A1107 " pdb=" C8 CLR A1107 " ideal model delta sigma weight residual 1.519 0.991 0.528 2.00e-02 2.50e+03 6.96e+02 bond pdb=" C14 CLR C1107 " pdb=" C8 CLR C1107 " ideal model delta sigma weight residual 1.519 0.993 0.526 2.00e-02 2.50e+03 6.90e+02 bond pdb=" C11 CLR A1107 " pdb=" C12 CLR A1107 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C11 CLR C1107 " pdb=" C12 CLR C1107 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C7 CLR C1107 " pdb=" C8 CLR C1107 " ideal model delta sigma weight residual 1.525 1.208 0.317 2.00e-02 2.50e+03 2.51e+02 ... (remaining 16651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.33: 22158 5.33 - 10.65: 241 10.65 - 15.98: 31 15.98 - 21.30: 3 21.30 - 26.63: 3 Bond angle restraints: 22436 Sorted by residual: angle pdb=" C12 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 111.01 84.38 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" C12 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C18 CLR C1107 " ideal model delta sigma weight residual 111.01 84.88 26.13 3.00e+00 1.11e-01 7.59e+01 angle pdb=" C14 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C18 CLR C1107 " ideal model delta sigma weight residual 112.24 90.51 21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C14 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 112.24 91.23 21.01 3.00e+00 1.11e-01 4.91e+01 angle pdb=" C12 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C17 CLR A1107 " ideal model delta sigma weight residual 116.52 133.32 -16.80 3.00e+00 1.11e-01 3.13e+01 ... (remaining 22431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9713 35.94 - 71.89: 258 71.89 - 107.83: 49 107.83 - 143.77: 5 143.77 - 179.71: 17 Dihedral angle restraints: 10042 sinusoidal: 4348 harmonic: 5694 Sorted by residual: dihedral pdb=" CA GLN C 508 " pdb=" C GLN C 508 " pdb=" N LYS C 509 " pdb=" CA LYS C 509 " ideal model delta harmonic sigma weight residual 180.00 142.34 37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA GLN A 508 " pdb=" C GLN A 508 " pdb=" N LYS A 509 " pdb=" CA LYS A 509 " ideal model delta harmonic sigma weight residual 180.00 142.46 37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA CYS A 589 " pdb=" C CYS A 589 " pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta harmonic sigma weight residual 180.00 145.43 34.57 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 10039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 2434 1.020 - 2.041: 2 2.041 - 3.061: 2 3.061 - 4.081: 0 4.081 - 5.102: 4 Chirality restraints: 2442 Sorted by residual: chirality pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C16 CLR A1107 " pdb=" C20 CLR A1107 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C17 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C16 CLR C1107 " pdb=" C20 CLR C1107 " both_signs ideal model delta sigma weight residual False 2.55 -2.51 5.06 2.00e-01 2.50e+01 6.40e+02 chirality pdb=" C9 CLR C1107 " pdb=" C10 CLR C1107 " pdb=" C11 CLR C1107 " pdb=" C8 CLR C1107 " both_signs ideal model delta sigma weight residual False -2.45 2.40 -4.84 2.00e-01 2.50e+01 5.87e+02 ... (remaining 2439 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 6ZP C1101 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.30e+01 pdb=" C03 6ZP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" C04 6ZP C1101 " 0.028 2.00e-02 2.50e+03 pdb=" C05 6ZP C1101 " 0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP C1101 " -0.031 2.00e-02 2.50e+03 pdb=" C07 6ZP C1101 " -0.023 2.00e-02 2.50e+03 pdb=" C08 6ZP C1101 " -0.004 2.00e-02 2.50e+03 pdb=" C09 6ZP C1101 " 0.025 2.00e-02 2.50e+03 pdb=" N01 6ZP C1101 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP A1101 " -0.035 2.00e-02 2.50e+03 3.08e-02 2.14e+01 pdb=" C03 6ZP A1101 " -0.028 2.00e-02 2.50e+03 pdb=" C04 6ZP A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C05 6ZP A1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP A1101 " 0.030 2.00e-02 2.50e+03 pdb=" C07 6ZP A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C08 6ZP A1101 " 0.004 2.00e-02 2.50e+03 pdb=" C09 6ZP A1101 " -0.025 2.00e-02 2.50e+03 pdb=" N01 6ZP A1101 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP B1101 " -0.022 2.00e-02 2.50e+03 1.81e-02 7.36e+00 pdb=" C03 6ZP B1101 " -0.016 2.00e-02 2.50e+03 pdb=" C04 6ZP B1101 " -0.013 2.00e-02 2.50e+03 pdb=" C05 6ZP B1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP B1101 " 0.019 2.00e-02 2.50e+03 pdb=" C07 6ZP B1101 " 0.014 2.00e-02 2.50e+03 pdb=" C08 6ZP B1101 " -0.006 2.00e-02 2.50e+03 pdb=" C09 6ZP B1101 " -0.011 2.00e-02 2.50e+03 pdb=" N01 6ZP B1101 " 0.037 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5060 2.84 - 3.36: 14584 3.36 - 3.87: 26916 3.87 - 4.39: 32360 4.39 - 4.90: 54069 Nonbonded interactions: 132989 Sorted by model distance: nonbonded pdb=" OH TYR D 533 " pdb=" O LEU D 577 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 533 " pdb=" O LEU B 577 " model vdw 2.329 3.040 nonbonded pdb=" OE1 GLN A 586 " pdb=" O HOH A1201 " model vdw 2.353 3.040 nonbonded pdb=" OE1 GLN C 586 " pdb=" O HOH C1201 " model vdw 2.355 3.040 nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D1201 " model vdw 2.359 3.040 ... (remaining 132984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 392 through 1034 or resid 1101 through 1107)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 392 through 817 or resid 1101 through 1105)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.260 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- 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 16656 Z= 0.946 Angle : 1.360 26.627 22436 Z= 0.647 Chirality : 0.232 5.102 2442 Planarity : 0.007 0.063 2694 Dihedral : 17.975 179.713 6392 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.89 % Favored : 95.80 % Rotamer: Outliers : 0.36 % Allowed : 4.77 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.13), residues: 1954 helix: -3.58 (0.09), residues: 1078 sheet: -2.07 (0.32), residues: 182 loop : -2.68 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 861 HIS 0.003 0.001 HIS C 883 PHE 0.019 0.002 PHE D 667 TYR 0.030 0.002 TYR D 702 ARG 0.009 0.001 ARG C 485 *********************** 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 fitting. rotamer outliers: 6 poor density : 323 time to evaluate : 1.705 Fit side-chains REVERT: A 697 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7773 (mptt) REVERT: B 594 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5361 (mmm-85) REVERT: B 708 MET cc_start: 0.7829 (mmp) cc_final: 0.7497 (mmm) REVERT: C 435 HIS cc_start: 0.7645 (m90) cc_final: 0.7261 (t70) REVERT: C 569 ASN cc_start: 0.2051 (OUTLIER) cc_final: 0.1831 (t0) REVERT: C 594 ARG cc_start: 0.5929 (tpt-90) cc_final: 0.4611 (tmm160) REVERT: C 637 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6691 (mt-10) REVERT: C 865 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6135 (mt-10) REVERT: D 431 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 585 MET cc_start: 0.5263 (mpt) cc_final: 0.4956 (mmt) REVERT: D 663 LYS cc_start: 0.7610 (mttp) cc_final: 0.7357 (mttp) REVERT: D 708 MET cc_start: 0.7775 (mmp) cc_final: 0.7435 (mmm) outliers start: 6 outliers final: 0 residues processed: 329 average time/residue: 1.4296 time to fit residues: 516.1266 Evaluate side-chains 194 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN A 587 GLN A 726 ASN A 747 ASN A 947 ASN A 990 ASN B 747 ASN B 756 GLN C 412 HIS C 587 GLN C 726 ASN C 747 ASN C 947 ASN C 990 ASN D 587 GLN D 756 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16656 Z= 0.233 Angle : 0.864 35.107 22436 Z= 0.385 Chirality : 0.062 1.564 2442 Planarity : 0.005 0.056 2694 Dihedral : 19.943 178.325 2802 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 2.62 % Allowed : 11.26 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 1954 helix: -0.39 (0.14), residues: 1074 sheet: -1.76 (0.34), residues: 186 loop : -2.22 (0.20), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 766 HIS 0.009 0.002 HIS C 412 PHE 0.014 0.002 PHE B 579 TYR 0.019 0.002 TYR A 469 ARG 0.006 0.001 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.7712 (mmm) cc_final: 0.7170 (mmm) REVERT: A 441 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8382 (ttmt) REVERT: A 697 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7898 (mptt) REVERT: A 924 MET cc_start: 0.4463 (mmm) cc_final: 0.4183 (mmm) REVERT: A 966 PHE cc_start: 0.7210 (m-80) cc_final: 0.6904 (m-80) REVERT: B 427 ASP cc_start: 0.8137 (m-30) cc_final: 0.7720 (m-30) REVERT: B 435 HIS cc_start: 0.7798 (m-70) cc_final: 0.6569 (t-90) REVERT: C 393 LYS cc_start: 0.7618 (mtmt) cc_final: 0.7154 (mttt) REVERT: C 435 HIS cc_start: 0.7730 (m90) cc_final: 0.7401 (t70) REVERT: C 594 ARG cc_start: 0.6280 (tpt-90) cc_final: 0.4985 (tmm160) REVERT: C 738 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7765 (tttp) REVERT: C 865 GLU cc_start: 0.6500 (mt-10) cc_final: 0.6201 (mt-10) REVERT: C 880 MET cc_start: 0.5406 (ptp) cc_final: 0.5173 (ptt) REVERT: C 924 MET cc_start: 0.6409 (mmt) cc_final: 0.5883 (mmm) REVERT: C 1031 ARG cc_start: 0.5565 (mmt180) cc_final: 0.5307 (ttm170) REVERT: D 397 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7836 (t) REVERT: D 435 HIS cc_start: 0.7752 (m-70) cc_final: 0.6557 (t-90) REVERT: D 587 GLN cc_start: 0.6514 (mm-40) cc_final: 0.5761 (mp10) outliers start: 44 outliers final: 14 residues processed: 251 average time/residue: 1.2366 time to fit residues: 348.1773 Evaluate side-chains 207 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 160 optimal weight: 0.3980 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 0.0010 chunk 144 optimal weight: 10.0000 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 587 GLN C 412 HIS C 587 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16656 Z= 0.292 Angle : 0.824 34.646 22436 Z= 0.371 Chirality : 0.063 1.562 2442 Planarity : 0.005 0.060 2694 Dihedral : 19.175 178.194 2800 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.22 % Allowed : 12.99 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 1954 helix: 0.84 (0.15), residues: 1070 sheet: -1.65 (0.34), residues: 198 loop : -2.12 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 766 HIS 0.027 0.002 HIS A 412 PHE 0.019 0.002 PHE C 541 TYR 0.019 0.002 TYR A 469 ARG 0.007 0.001 ARG B 453 *********************** 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 249 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 195 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8047 (mmm) cc_final: 0.7577 (mmm) REVERT: A 435 HIS cc_start: 0.7757 (m90) cc_final: 0.7383 (t70) REVERT: A 458 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7508 (mmtp) REVERT: A 594 ARG cc_start: 0.6752 (tpt-90) cc_final: 0.5828 (ttp-170) REVERT: A 697 LYS cc_start: 0.8278 (mtmm) cc_final: 0.8050 (mptt) REVERT: A 966 PHE cc_start: 0.7133 (m-80) cc_final: 0.6870 (m-80) REVERT: A 1002 LYS cc_start: 0.6274 (tppp) cc_final: 0.5820 (tttp) REVERT: A 1023 MET cc_start: 0.6249 (mmt) cc_final: 0.6031 (mmm) REVERT: B 397 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7819 (t) REVERT: B 435 HIS cc_start: 0.7768 (m-70) cc_final: 0.6536 (t-90) REVERT: B 594 ARG cc_start: 0.6494 (mtt90) cc_final: 0.5550 (mmm-85) REVERT: C 393 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7262 (mttt) REVERT: C 435 HIS cc_start: 0.7812 (m90) cc_final: 0.7398 (t70) REVERT: C 594 ARG cc_start: 0.6688 (tpt-90) cc_final: 0.5376 (tmm160) REVERT: C 865 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6163 (mt-10) REVERT: C 880 MET cc_start: 0.5414 (ptp) cc_final: 0.5160 (ptt) REVERT: C 884 SER cc_start: 0.7205 (OUTLIER) cc_final: 0.6878 (m) REVERT: C 924 MET cc_start: 0.6285 (mmt) cc_final: 0.5956 (mmm) REVERT: C 1002 LYS cc_start: 0.6184 (tppp) cc_final: 0.5889 (tttp) REVERT: D 397 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7876 (t) REVERT: D 435 HIS cc_start: 0.7758 (m-70) cc_final: 0.6506 (t-90) REVERT: D 587 GLN cc_start: 0.6683 (mm-40) cc_final: 0.6298 (mp10) REVERT: D 730 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8055 (mtpm) outliers start: 54 outliers final: 18 residues processed: 234 average time/residue: 1.3264 time to fit residues: 344.8371 Evaluate side-chains 208 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 527 MET 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 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 D residue 397 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 730 LYS Chi-restraints excluded: chain D residue 741 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16656 Z= 0.167 Angle : 0.748 34.509 22436 Z= 0.328 Chirality : 0.061 1.587 2442 Planarity : 0.004 0.055 2694 Dihedral : 18.813 178.435 2800 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.92 % Allowed : 14.06 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1954 helix: 1.62 (0.16), residues: 1066 sheet: -1.59 (0.33), residues: 200 loop : -1.80 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 766 HIS 0.010 0.001 HIS C 412 PHE 0.019 0.001 PHE A 960 TYR 0.020 0.001 TYR A1001 ARG 0.007 0.001 ARG B 453 *********************** 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 234 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8014 (mmm) cc_final: 0.7422 (mmm) REVERT: A 435 HIS cc_start: 0.7820 (m90) cc_final: 0.7452 (t70) REVERT: A 697 LYS cc_start: 0.8251 (mtmm) cc_final: 0.8041 (mptt) REVERT: A 966 PHE cc_start: 0.7098 (m-80) cc_final: 0.6826 (m-80) REVERT: A 1002 LYS cc_start: 0.6216 (tppp) cc_final: 0.5758 (tttp) REVERT: B 587 GLN cc_start: 0.5679 (OUTLIER) cc_final: 0.4744 (mp10) REVERT: B 594 ARG cc_start: 0.6582 (mtt90) cc_final: 0.6227 (mmt90) REVERT: C 393 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7339 (mttt) REVERT: C 435 HIS cc_start: 0.7820 (m90) cc_final: 0.7429 (t70) REVERT: C 509 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5831 (tttm) REVERT: C 834 ARG cc_start: 0.6426 (ptm160) cc_final: 0.5861 (mtm180) REVERT: C 865 GLU cc_start: 0.6342 (mt-10) cc_final: 0.6134 (tt0) REVERT: C 884 SER cc_start: 0.7176 (OUTLIER) cc_final: 0.6888 (m) REVERT: C 924 MET cc_start: 0.6270 (mmt) cc_final: 0.5973 (mmm) REVERT: C 1002 LYS cc_start: 0.6026 (tppp) cc_final: 0.5674 (tttp) REVERT: D 435 HIS cc_start: 0.7741 (m-70) cc_final: 0.6508 (t-90) REVERT: D 587 GLN cc_start: 0.6671 (mm-40) cc_final: 0.6386 (mp10) outliers start: 49 outliers final: 19 residues processed: 223 average time/residue: 1.3539 time to fit residues: 334.4214 Evaluate side-chains 192 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1032 TYR 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 699 LYS 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 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 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.0070 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16656 Z= 0.222 Angle : 0.759 34.226 22436 Z= 0.336 Chirality : 0.062 1.606 2442 Planarity : 0.004 0.059 2694 Dihedral : 18.684 179.079 2800 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.22 % Allowed : 14.42 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1954 helix: 1.86 (0.16), residues: 1064 sheet: -1.51 (0.34), residues: 200 loop : -1.74 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 766 HIS 0.009 0.001 HIS C 412 PHE 0.023 0.001 PHE A 960 TYR 0.022 0.001 TYR A1001 ARG 0.008 0.001 ARG D 453 *********************** 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 228 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8016 (mmm) cc_final: 0.7469 (mmm) REVERT: A 435 HIS cc_start: 0.7814 (m90) cc_final: 0.7412 (t70) REVERT: A 952 ARG cc_start: 0.5154 (mtp180) cc_final: 0.4905 (tmm160) REVERT: A 1002 LYS cc_start: 0.6271 (tppp) cc_final: 0.5751 (tttp) REVERT: B 594 ARG cc_start: 0.6645 (mtt90) cc_final: 0.6268 (mmt90) REVERT: B 663 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6909 (mttp) REVERT: C 393 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7338 (mttt) REVERT: C 411 ASN cc_start: 0.6647 (p0) cc_final: 0.6272 (p0) REVERT: C 435 HIS cc_start: 0.7852 (m90) cc_final: 0.7400 (t70) REVERT: C 509 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5781 (tttm) REVERT: C 524 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: C 834 ARG cc_start: 0.6095 (ptm160) cc_final: 0.5869 (mtm180) REVERT: C 884 SER cc_start: 0.7187 (OUTLIER) cc_final: 0.6910 (m) REVERT: C 924 MET cc_start: 0.6251 (mmt) cc_final: 0.5932 (mmm) REVERT: C 1002 LYS cc_start: 0.6289 (tppp) cc_final: 0.5871 (tttp) REVERT: D 435 HIS cc_start: 0.7779 (m-70) cc_final: 0.6473 (t-90) REVERT: D 587 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6543 (mp10) REVERT: D 599 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.5591 (mmt-90) outliers start: 54 outliers final: 24 residues processed: 211 average time/residue: 1.3430 time to fit residues: 316.1437 Evaluate side-chains 196 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain B residue 510 SER 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 B residue 699 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 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 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 719 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 0.0570 chunk 88 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 overall best weight: 0.6102 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16656 Z= 0.183 Angle : 0.742 34.017 22436 Z= 0.325 Chirality : 0.062 1.620 2442 Planarity : 0.004 0.056 2694 Dihedral : 18.535 179.982 2800 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.34 % Allowed : 14.66 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1954 helix: 1.98 (0.16), residues: 1070 sheet: -1.26 (0.35), residues: 196 loop : -1.66 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 766 HIS 0.011 0.001 HIS C 412 PHE 0.024 0.001 PHE A 960 TYR 0.028 0.001 TYR C1032 ARG 0.008 0.000 ARG B 453 *********************** 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 226 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 170 time to evaluate : 1.880 Fit side-chains REVERT: A 392 GLN cc_start: 0.5467 (OUTLIER) cc_final: 0.5199 (pp30) REVERT: A 408 MET cc_start: 0.7984 (mmm) cc_final: 0.7449 (mmm) REVERT: A 435 HIS cc_start: 0.7832 (m90) cc_final: 0.7410 (t70) REVERT: A 571 PHE cc_start: 0.6154 (m-10) cc_final: 0.5784 (m-80) REVERT: A 952 ARG cc_start: 0.5129 (mtp180) cc_final: 0.4894 (tmm160) REVERT: A 1002 LYS cc_start: 0.6304 (tppp) cc_final: 0.5732 (tttp) REVERT: B 594 ARG cc_start: 0.6649 (mtt90) cc_final: 0.5737 (mmm-85) REVERT: C 393 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7395 (mttt) REVERT: C 411 ASN cc_start: 0.6571 (p0) cc_final: 0.6243 (p0) REVERT: C 435 HIS cc_start: 0.7842 (m90) cc_final: 0.7407 (t70) REVERT: C 509 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.5839 (tttm) REVERT: C 524 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: C 669 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7578 (ptmm) REVERT: C 834 ARG cc_start: 0.6149 (ptm160) cc_final: 0.5906 (mtm180) REVERT: C 884 SER cc_start: 0.7155 (OUTLIER) cc_final: 0.6887 (m) REVERT: C 924 MET cc_start: 0.6252 (mmt) cc_final: 0.5913 (mmm) REVERT: C 1002 LYS cc_start: 0.6234 (tppp) cc_final: 0.5798 (tttp) REVERT: D 587 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6568 (mp10) REVERT: D 599 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.5351 (mmt-90) outliers start: 56 outliers final: 28 residues processed: 212 average time/residue: 1.3800 time to fit residues: 324.1242 Evaluate side-chains 201 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN 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 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR 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 699 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain 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 719 ASP Chi-restraints excluded: chain D residue 741 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 190 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16656 Z= 0.189 Angle : 0.736 33.700 22436 Z= 0.321 Chirality : 0.062 1.644 2442 Planarity : 0.004 0.056 2694 Dihedral : 18.362 179.225 2800 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.16 % Allowed : 15.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1954 helix: 2.10 (0.16), residues: 1070 sheet: -1.10 (0.35), residues: 194 loop : -1.60 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1005 HIS 0.010 0.001 HIS C 412 PHE 0.027 0.001 PHE A 960 TYR 0.023 0.001 TYR A1001 ARG 0.005 0.000 ARG D 453 *********************** 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 229 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 176 time to evaluate : 1.713 Fit side-chains REVERT: A 392 GLN cc_start: 0.5503 (OUTLIER) cc_final: 0.5213 (pp30) REVERT: A 408 MET cc_start: 0.7957 (mmm) cc_final: 0.7380 (mmm) REVERT: A 435 HIS cc_start: 0.7807 (m90) cc_final: 0.7390 (t70) REVERT: A 571 PHE cc_start: 0.6029 (m-10) cc_final: 0.5686 (m-80) REVERT: A 1002 LYS cc_start: 0.6441 (tppp) cc_final: 0.5745 (tttp) REVERT: B 594 ARG cc_start: 0.6672 (mtt90) cc_final: 0.5639 (mmm-85) REVERT: C 393 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7438 (mttt) REVERT: C 411 ASN cc_start: 0.6621 (p0) cc_final: 0.6338 (p0) REVERT: C 435 HIS cc_start: 0.7847 (m90) cc_final: 0.7414 (t70) REVERT: C 509 LYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5918 (tttm) REVERT: C 524 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: C 635 SER cc_start: 0.8526 (m) cc_final: 0.8193 (p) REVERT: C 884 SER cc_start: 0.7114 (OUTLIER) cc_final: 0.6834 (m) REVERT: C 907 MET cc_start: 0.3279 (mmt) cc_final: 0.2175 (mtt) REVERT: C 924 MET cc_start: 0.6209 (mmt) cc_final: 0.5941 (mmm) REVERT: C 1002 LYS cc_start: 0.6320 (tppp) cc_final: 0.5829 (tttp) REVERT: D 599 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.5581 (mmt-90) outliers start: 53 outliers final: 29 residues processed: 213 average time/residue: 1.2990 time to fit residues: 307.3035 Evaluate side-chains 197 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN 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 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR 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 699 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 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 719 ASP Chi-restraints excluded: chain D residue 741 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.0040 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16656 Z= 0.166 Angle : 0.726 33.476 22436 Z= 0.315 Chirality : 0.062 1.661 2442 Planarity : 0.004 0.054 2694 Dihedral : 18.206 179.978 2800 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.92 % Allowed : 16.09 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1954 helix: 2.20 (0.16), residues: 1070 sheet: -1.02 (0.35), residues: 194 loop : -1.53 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 606 HIS 0.011 0.001 HIS C 412 PHE 0.022 0.001 PHE A 960 TYR 0.024 0.001 TYR A1001 ARG 0.005 0.000 ARG D 453 *********************** 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 fitting. rotamer outliers: 49 poor density : 178 time to evaluate : 1.817 Fit side-chains REVERT: A 392 GLN cc_start: 0.5515 (OUTLIER) cc_final: 0.5183 (pp30) REVERT: A 408 MET cc_start: 0.7914 (mmm) cc_final: 0.7332 (mmm) REVERT: A 435 HIS cc_start: 0.7791 (m90) cc_final: 0.7378 (t70) REVERT: A 571 PHE cc_start: 0.5901 (m-10) cc_final: 0.5558 (m-80) REVERT: A 635 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8224 (p) REVERT: A 907 MET cc_start: 0.3535 (ttt) cc_final: 0.2927 (mpt) REVERT: A 1002 LYS cc_start: 0.6439 (tppp) cc_final: 0.5732 (tttp) REVERT: B 594 ARG cc_start: 0.6740 (mtt90) cc_final: 0.5725 (mmm-85) REVERT: C 392 GLN cc_start: 0.5462 (pp30) cc_final: 0.5251 (pp30) REVERT: C 393 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7343 (mttt) REVERT: C 435 HIS cc_start: 0.7837 (m90) cc_final: 0.7402 (t70) REVERT: C 524 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: C 635 SER cc_start: 0.8516 (m) cc_final: 0.8216 (p) REVERT: C 669 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7726 (ptmm) REVERT: C 884 SER cc_start: 0.6973 (OUTLIER) cc_final: 0.6703 (m) REVERT: C 907 MET cc_start: 0.3097 (mmt) cc_final: 0.2015 (mtt) REVERT: C 924 MET cc_start: 0.6142 (mmt) cc_final: 0.5904 (mmm) REVERT: C 1002 LYS cc_start: 0.6381 (tppp) cc_final: 0.5889 (tttp) REVERT: D 594 ARG cc_start: 0.6685 (mtt90) cc_final: 0.5692 (mmm-85) REVERT: D 599 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.5455 (mmt-90) REVERT: D 663 LYS cc_start: 0.7331 (mtmt) cc_final: 0.7051 (mtmm) outliers start: 49 outliers final: 28 residues processed: 213 average time/residue: 1.3877 time to fit residues: 327.5980 Evaluate side-chains 207 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN 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 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 719 ASP 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 173 optimal weight: 0.2980 chunk 182 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 160 optimal weight: 6.9990 chunk 168 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16656 Z= 0.147 Angle : 0.715 33.231 22436 Z= 0.309 Chirality : 0.062 1.674 2442 Planarity : 0.004 0.053 2694 Dihedral : 18.019 179.538 2800 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.56 % Allowed : 17.04 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1954 helix: 2.34 (0.16), residues: 1070 sheet: -1.02 (0.36), residues: 186 loop : -1.42 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 606 HIS 0.011 0.001 HIS C 412 PHE 0.021 0.001 PHE A 960 TYR 0.025 0.001 TYR A1001 ARG 0.006 0.000 ARG D 453 *********************** 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 219 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 1.780 Fit side-chains REVERT: A 392 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.5176 (pp30) REVERT: A 408 MET cc_start: 0.7852 (mmm) cc_final: 0.7314 (mmm) REVERT: A 435 HIS cc_start: 0.7791 (m90) cc_final: 0.7391 (t70) REVERT: A 571 PHE cc_start: 0.5657 (m-10) cc_final: 0.5359 (m-80) REVERT: A 635 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 907 MET cc_start: 0.3503 (ttt) cc_final: 0.2919 (mpt) REVERT: A 1002 LYS cc_start: 0.6440 (tppp) cc_final: 0.5771 (tttp) REVERT: B 503 MET cc_start: 0.9252 (ttp) cc_final: 0.8987 (ttm) REVERT: B 594 ARG cc_start: 0.6667 (mtt90) cc_final: 0.5710 (mmm-85) REVERT: C 392 GLN cc_start: 0.5441 (OUTLIER) cc_final: 0.5199 (pp30) REVERT: C 393 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7411 (mttt) REVERT: C 435 HIS cc_start: 0.7823 (m90) cc_final: 0.7388 (t-90) REVERT: C 524 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: C 635 SER cc_start: 0.8495 (m) cc_final: 0.8228 (p) REVERT: C 669 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7771 (ptmm) REVERT: C 884 SER cc_start: 0.6941 (OUTLIER) cc_final: 0.6675 (m) REVERT: C 907 MET cc_start: 0.3085 (mmt) cc_final: 0.2021 (mtt) REVERT: C 924 MET cc_start: 0.6033 (mmt) cc_final: 0.5806 (mmm) REVERT: C 1002 LYS cc_start: 0.6370 (tppp) cc_final: 0.5894 (tttp) REVERT: C 1029 MET cc_start: 0.5677 (mmm) cc_final: 0.5428 (mmm) REVERT: D 453 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7491 (ttp80) REVERT: D 527 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6446 (mtt) REVERT: D 594 ARG cc_start: 0.6669 (mtt90) cc_final: 0.5753 (mmm-85) REVERT: D 599 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5422 (mmt-90) outliers start: 43 outliers final: 27 residues processed: 207 average time/residue: 1.3445 time to fit residues: 307.9411 Evaluate side-chains 202 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN 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 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 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 C residue 392 GLN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 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 527 MET Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 719 ASP 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 188 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16656 Z= 0.204 Angle : 0.741 33.340 22436 Z= 0.324 Chirality : 0.063 1.676 2442 Planarity : 0.004 0.055 2694 Dihedral : 18.023 179.696 2800 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.21 % Allowed : 17.52 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1954 helix: 2.25 (0.16), residues: 1068 sheet: -1.01 (0.36), residues: 186 loop : -1.46 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 606 HIS 0.010 0.001 HIS C 412 PHE 0.020 0.001 PHE A 960 TYR 0.024 0.001 TYR A1001 ARG 0.005 0.000 ARG B 453 ********************** 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 211 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 2.062 Fit side-chains REVERT: A 392 GLN cc_start: 0.5520 (OUTLIER) cc_final: 0.5172 (pp30) REVERT: A 408 MET cc_start: 0.7884 (mmm) cc_final: 0.7335 (mmm) REVERT: A 435 HIS cc_start: 0.7795 (m90) cc_final: 0.7359 (t-90) REVERT: A 571 PHE cc_start: 0.5579 (m-10) cc_final: 0.5362 (m-80) REVERT: A 635 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 697 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (mptt) REVERT: A 907 MET cc_start: 0.3501 (ttt) cc_final: 0.2919 (mpt) REVERT: A 966 PHE cc_start: 0.6909 (m-80) cc_final: 0.6250 (m-80) REVERT: A 1002 LYS cc_start: 0.6656 (tppp) cc_final: 0.5926 (tttp) REVERT: B 503 MET cc_start: 0.9379 (ttp) cc_final: 0.9089 (ttm) REVERT: B 594 ARG cc_start: 0.6759 (mtt90) cc_final: 0.5853 (mmm-85) REVERT: C 392 GLN cc_start: 0.5519 (OUTLIER) cc_final: 0.5246 (pp30) REVERT: C 435 HIS cc_start: 0.7839 (m90) cc_final: 0.7402 (t70) REVERT: C 524 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: C 635 SER cc_start: 0.8531 (m) cc_final: 0.8215 (p) REVERT: C 669 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7805 (ptmm) REVERT: C 884 SER cc_start: 0.7042 (OUTLIER) cc_final: 0.6788 (m) REVERT: C 907 MET cc_start: 0.3081 (mmt) cc_final: 0.2045 (mtt) REVERT: C 1002 LYS cc_start: 0.6278 (tppp) cc_final: 0.5766 (tttp) REVERT: C 1029 MET cc_start: 0.5640 (mmm) cc_final: 0.5371 (mmm) REVERT: D 527 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6484 (mtt) REVERT: D 594 ARG cc_start: 0.6662 (mtt90) cc_final: 0.5721 (mmm-85) REVERT: D 599 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5589 (mmt-90) outliers start: 37 outliers final: 26 residues processed: 199 average time/residue: 1.3891 time to fit residues: 305.8281 Evaluate side-chains 206 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN 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 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 697 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 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 527 MET Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 719 ASP 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 167 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 161 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 138 optimal weight: 3.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138425 restraints weight = 17813.969| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.01 r_work: 0.3175 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16656 Z= 0.202 Angle : 0.744 33.289 22436 Z= 0.325 Chirality : 0.063 1.675 2442 Planarity : 0.004 0.058 2694 Dihedral : 17.966 179.342 2800 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.32 % Allowed : 17.46 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1954 helix: 2.23 (0.16), residues: 1068 sheet: -1.06 (0.36), residues: 186 loop : -1.46 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 606 HIS 0.010 0.001 HIS C 412 PHE 0.019 0.001 PHE B 579 TYR 0.024 0.001 TYR C1001 ARG 0.005 0.000 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6199.88 seconds wall clock time: 112 minutes 28.95 seconds (6748.95 seconds total)