Starting phenix.real_space_refine on Fri May 16 21:59:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fws_29517/05_2025/8fws_29517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fws_29517/05_2025/8fws_29517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fws_29517/05_2025/8fws_29517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fws_29517/05_2025/8fws_29517.map" model { file = "/net/cci-nas-00/data/ceres_data/8fws_29517/05_2025/8fws_29517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fws_29517/05_2025/8fws_29517.cif" } resolution = 3.23 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= 0.004 sd= 0.085 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: 8 Type Number sf(0) Gaussians P 16 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 6 4.78 5 C 9432 2.51 5 N 2190 2.21 5 O 2686 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14416 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 362 Unusual residues: {' CL': 1, ' NA': 3, '2J9': 2, 'NAG': 1, 'POV': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 256 Unusual residues: {' CL': 1, ' NA': 1, '2J9': 2, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.92, per 1000 atoms: 0.62 Number of scatterers: 14416 At special positions: 0 Unit cell: (115.625, 132.275, 136.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 80 16.00 P 16 15.00 Na 6 11.00 F 4 9.00 O 2686 8.00 N 2190 7.00 C 9432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS B 595 " distance=2.00 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.02 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.02 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=2.06 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.02 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.02 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 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA I 3 " - " BMA I 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1006 " - " ASN A 751 " " NAG C1006 " - " ASN C 751 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 546 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 18 sheets defined 49.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.946A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.021A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.696A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.516A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 631 through 665 removed outlier: 3.575A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.039A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.688A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.710A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.903A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.605A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.538A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.517A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.680A pdb=" N ASN B 557 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.729A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.618A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.570A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.648A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 711 removed outlier: 3.590A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.553A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.704A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.856A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.731A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 845 " --> pdb=" O GLU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.946A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 4.022A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.695A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.516A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 631 through 665 removed outlier: 3.576A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 removed outlier: 4.040A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.688A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 712 Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 748 removed outlier: 3.710A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.902A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.604A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 799 Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.538A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.518A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.679A pdb=" N ASN D 557 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.729A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.618A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.569A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.648A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 711 removed outlier: 3.590A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.553A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.703A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 789 removed outlier: 3.857A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 794 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.731A pdb=" N VAL D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 845 " --> pdb=" O GLU D 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.163A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 683 removed outlier: 7.194A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.558A pdb=" N GLU B 460 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.247A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.163A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 681 through 683 removed outlier: 7.194A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 445 through 446 removed outlier: 3.558A pdb=" N GLU D 460 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB8, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.248A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1620 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: 4.18 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2224 1.31 - 1.44: 3912 1.44 - 1.57: 8392 1.57 - 1.70: 48 1.70 - 1.83: 132 Bond restraints: 14708 Sorted by residual: bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 C1002 " pdb=" SAP 2J9 C1002 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 C1001 " pdb=" SAP 2J9 C1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 14703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.58: 19590 6.58 - 13.16: 180 13.16 - 19.73: 4 19.73 - 26.31: 0 26.31 - 32.89: 8 Bond angle restraints: 19782 Sorted by residual: angle pdb=" CAH 2J9 A1009 " pdb=" CAN 2J9 A1009 " pdb=" NAO 2J9 A1009 " ideal model delta sigma weight residual 117.67 150.56 -32.89 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CAH 2J9 C1001 " pdb=" CAN 2J9 C1001 " pdb=" NAO 2J9 C1001 " ideal model delta sigma weight residual 117.67 150.26 -32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 C1002 " pdb=" CAN 2J9 C1002 " pdb=" NAO 2J9 C1002 " ideal model delta sigma weight residual 117.67 149.75 -32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.74 -31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.24 -31.57 3.00e+00 1.11e-01 1.11e+02 ... (remaining 19777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 8509 28.61 - 57.22: 474 57.22 - 85.82: 114 85.82 - 114.43: 37 114.43 - 143.04: 14 Dihedral angle restraints: 9148 sinusoidal: 4308 harmonic: 4840 Sorted by residual: dihedral pdb=" CA TYR D 478 " pdb=" C TYR D 478 " pdb=" N GLU D 479 " pdb=" CA GLU D 479 " ideal model delta harmonic sigma weight residual -180.00 -129.43 -50.57 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA TYR B 478 " pdb=" C TYR B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta harmonic sigma weight residual -180.00 -129.48 -50.52 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA VAL B 716 " pdb=" C VAL B 716 " pdb=" N LEU B 717 " pdb=" CA LEU B 717 " ideal model delta harmonic sigma weight residual 180.00 141.31 38.69 0 5.00e+00 4.00e-02 5.99e+01 ... (remaining 9145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.464: 2154 0.464 - 0.927: 0 0.927 - 1.391: 0 1.391 - 1.854: 0 1.854 - 2.318: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 A1009 " pdb=" CAG 2J9 A1009 " pdb=" CAH 2J9 A1009 " pdb=" NAO 2J9 A1009 " both_signs ideal model delta sigma weight residual True 2.32 -0.00 2.32 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 C1001 " pdb=" CAG 2J9 C1001 " pdb=" CAH 2J9 C1001 " pdb=" NAO 2J9 C1001 " both_signs ideal model delta sigma weight residual True 2.32 0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 C1002 " pdb=" CAG 2J9 C1002 " pdb=" CAH 2J9 C1002 " pdb=" NAO 2J9 C1002 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 ... (remaining 2155 not shown) Planarity restraints: 2398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 716 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL D 716 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL D 716 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 717 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 716 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL B 716 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL B 716 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 717 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO B 516 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " -0.033 5.00e-02 4.00e+02 ... (remaining 2395 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3232 2.78 - 3.31: 12234 3.31 - 3.84: 22352 3.84 - 4.37: 27840 4.37 - 4.90: 47421 Nonbonded interactions: 113079 Sorted by model distance: nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.273 3.040 nonbonded pdb=" O SER C 632 " pdb=" OG SER D 834 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 585 " pdb=" OE2 GLU B 841 " model vdw 2.307 3.040 ... (remaining 113074 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 431 through 850 or resid 1003)) selection = (chain 'B' and (resid 431 through 850 or resid 1003)) selection = (chain 'C' and (resid 431 through 850 or resid 1003)) selection = (chain 'D' and (resid 431 through 850 or resid 1003)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.410 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 : 0.012 0.203 14732 Z= 0.580 Angle : 1.648 32.889 19848 Z= 0.776 Chirality : 0.116 2.318 2158 Planarity : 0.007 0.058 2390 Dihedral : 19.895 143.040 6034 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.49 % Favored : 91.15 % Rotamer: Outliers : 0.55 % Allowed : 4.28 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.96 (0.13), residues: 1672 helix: -4.37 (0.07), residues: 802 sheet: -3.11 (0.38), residues: 134 loop : -3.49 (0.17), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 706 HIS 0.005 0.001 HIS D 593 PHE 0.029 0.003 PHE D 446 TYR 0.028 0.003 TYR B 702 ARG 0.008 0.001 ARG B 713 Details of bonding type rmsd link_NAG-ASN : bond 0.01837 ( 8) link_NAG-ASN : angle 7.93277 ( 24) link_BETA1-4 : bond 0.01669 ( 8) link_BETA1-4 : angle 4.06420 ( 24) hydrogen bonds : bond 0.30928 ( 558) hydrogen bonds : angle 11.22768 ( 1620) SS BOND : bond 0.01844 ( 6) SS BOND : angle 1.36329 ( 12) link_BETA1-3 : bond 0.00161 ( 2) link_BETA1-3 : angle 3.28805 ( 6) covalent geometry : bond 0.01180 (14708) covalent geometry : angle 1.61966 (19782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 356 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7629 (t70) cc_final: 0.7262 (t0) REVERT: A 468 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6806 (mtm110) REVERT: A 591 ASN cc_start: 0.8028 (t160) cc_final: 0.7782 (t0) REVERT: A 719 LYS cc_start: 0.7853 (pptt) cc_final: 0.7174 (mtpp) REVERT: A 751 ASN cc_start: 0.6673 (m-40) cc_final: 0.5963 (t0) REVERT: A 776 ASP cc_start: 0.7460 (m-30) cc_final: 0.6979 (m-30) REVERT: A 796 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7208 (mt-10) REVERT: A 845 LYS cc_start: 0.6977 (tptt) cc_final: 0.6703 (tppp) REVERT: B 790 LYS cc_start: 0.7862 (mptp) cc_final: 0.7503 (mmmt) REVERT: B 818 GLN cc_start: 0.8085 (pt0) cc_final: 0.7783 (pm20) REVERT: C 468 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6726 (mtm110) REVERT: C 487 LYS cc_start: 0.7416 (mtpp) cc_final: 0.7138 (mtmt) REVERT: C 584 PHE cc_start: 0.6603 (t80) cc_final: 0.6359 (t80) REVERT: C 591 ASN cc_start: 0.8102 (t160) cc_final: 0.7722 (t0) REVERT: C 677 GLN cc_start: 0.6669 (mp-120) cc_final: 0.6240 (mp10) REVERT: C 696 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7452 (mtmt) REVERT: C 719 LYS cc_start: 0.8313 (pptt) cc_final: 0.7641 (mtpp) REVERT: C 726 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7271 (mm-40) REVERT: C 776 ASP cc_start: 0.7331 (m-30) cc_final: 0.6747 (m-30) REVERT: C 796 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6992 (mt-10) REVERT: C 845 LYS cc_start: 0.6933 (tptt) cc_final: 0.6686 (tppt) REVERT: D 492 ASP cc_start: 0.7492 (t70) cc_final: 0.6809 (m-30) REVERT: D 790 LYS cc_start: 0.7758 (mptp) cc_final: 0.7417 (mmmt) outliers start: 8 outliers final: 0 residues processed: 362 average time/residue: 0.3157 time to fit residues: 157.6621 Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 591 ASN A 596 ASN A 604 ASN B 456 ASN B 621 GLN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 621 GLN D 456 ASN D 604 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146136 restraints weight = 15970.656| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.97 r_work: 0.3399 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14732 Z= 0.183 Angle : 0.794 9.634 19848 Z= 0.389 Chirality : 0.047 0.171 2158 Planarity : 0.006 0.048 2390 Dihedral : 22.729 139.542 2894 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.13 % Favored : 91.39 % Rotamer: Outliers : 2.14 % Allowed : 10.15 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.11 (0.16), residues: 1672 helix: -2.26 (0.14), residues: 846 sheet: -3.03 (0.33), residues: 158 loop : -3.12 (0.20), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 706 HIS 0.003 0.001 HIS D 593 PHE 0.017 0.002 PHE B 735 TYR 0.022 0.002 TYR D 478 ARG 0.007 0.001 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 8) link_NAG-ASN : angle 5.53071 ( 24) link_BETA1-4 : bond 0.00803 ( 8) link_BETA1-4 : angle 2.67889 ( 24) hydrogen bonds : bond 0.04914 ( 558) hydrogen bonds : angle 5.13625 ( 1620) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.54472 ( 12) link_BETA1-3 : bond 0.00580 ( 2) link_BETA1-3 : angle 3.71397 ( 6) covalent geometry : bond 0.00429 (14708) covalent geometry : angle 0.76182 (19782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 TYR cc_start: 0.8258 (m-10) cc_final: 0.7820 (m-10) REVERT: A 715 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7167 (p) REVERT: A 719 LYS cc_start: 0.7958 (pptt) cc_final: 0.7708 (mtpp) REVERT: B 691 MET cc_start: 0.7714 (ttp) cc_final: 0.7439 (ttt) REVERT: B 790 LYS cc_start: 0.7813 (mptp) cc_final: 0.7504 (mmmt) REVERT: B 825 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8173 (mt) REVERT: C 584 PHE cc_start: 0.6890 (t80) cc_final: 0.6649 (t80) REVERT: C 696 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7422 (mtmt) REVERT: C 719 LYS cc_start: 0.8258 (pptt) cc_final: 0.8044 (mtpp) REVERT: D 691 MET cc_start: 0.7684 (tmm) cc_final: 0.7464 (ttt) REVERT: D 790 LYS cc_start: 0.7690 (mptp) cc_final: 0.7268 (mmmt) REVERT: D 819 ASN cc_start: 0.8279 (m110) cc_final: 0.8009 (m-40) REVERT: D 825 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8211 (mt) outliers start: 31 outliers final: 17 residues processed: 215 average time/residue: 0.2757 time to fit residues: 85.4190 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN A 747 GLN B 456 ASN B 495 ASN D 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.175371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146798 restraints weight = 15888.073| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.84 r_work: 0.3347 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14732 Z= 0.149 Angle : 0.717 11.014 19848 Z= 0.344 Chirality : 0.045 0.181 2158 Planarity : 0.004 0.043 2390 Dihedral : 20.911 140.502 2894 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.48 % Favored : 92.05 % Rotamer: Outliers : 2.69 % Allowed : 11.74 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.73 (0.19), residues: 1672 helix: -0.77 (0.17), residues: 852 sheet: -2.84 (0.34), residues: 154 loop : -2.91 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 798 HIS 0.003 0.000 HIS B 593 PHE 0.017 0.002 PHE D 579 TYR 0.021 0.002 TYR D 844 ARG 0.007 0.001 ARG D 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 8) link_NAG-ASN : angle 4.93890 ( 24) link_BETA1-4 : bond 0.00715 ( 8) link_BETA1-4 : angle 2.65986 ( 24) hydrogen bonds : bond 0.03799 ( 558) hydrogen bonds : angle 4.40426 ( 1620) SS BOND : bond 0.00245 ( 6) SS BOND : angle 1.86340 ( 12) link_BETA1-3 : bond 0.00562 ( 2) link_BETA1-3 : angle 3.42291 ( 6) covalent geometry : bond 0.00352 (14708) covalent geometry : angle 0.68683 (19782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7733 (t70) cc_final: 0.7321 (t0) REVERT: A 566 TYR cc_start: 0.8412 (m-10) cc_final: 0.7883 (m-10) REVERT: A 664 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8187 (mtt) REVERT: A 703 ASP cc_start: 0.7349 (t70) cc_final: 0.6911 (t0) REVERT: B 669 ASP cc_start: 0.8061 (t70) cc_final: 0.7675 (t70) REVERT: B 677 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.5890 (mp10) REVERT: B 691 MET cc_start: 0.7814 (ttp) cc_final: 0.7512 (ttt) REVERT: B 790 LYS cc_start: 0.7926 (mptp) cc_final: 0.7506 (tptt) REVERT: B 825 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (mt) REVERT: C 584 PHE cc_start: 0.6847 (t80) cc_final: 0.6579 (t80) REVERT: C 661 VAL cc_start: 0.8544 (t) cc_final: 0.8258 (m) REVERT: C 696 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7424 (mtmt) REVERT: C 719 LYS cc_start: 0.8394 (pptt) cc_final: 0.8071 (mtpp) REVERT: C 845 LYS cc_start: 0.7232 (tppt) cc_final: 0.6743 (tppp) REVERT: D 691 MET cc_start: 0.7635 (tmm) cc_final: 0.7431 (ttt) REVERT: D 705 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8496 (mtt) REVERT: D 743 GLU cc_start: 0.8341 (mp0) cc_final: 0.7957 (mp0) REVERT: D 790 LYS cc_start: 0.7711 (mptp) cc_final: 0.7281 (tptt) REVERT: D 819 ASN cc_start: 0.8465 (m110) cc_final: 0.8100 (m110) REVERT: D 825 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8172 (mt) outliers start: 39 outliers final: 23 residues processed: 186 average time/residue: 0.2780 time to fit residues: 75.4692 Evaluate side-chains 174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.173248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145445 restraints weight = 16166.538| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3328 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14732 Z= 0.157 Angle : 0.696 9.857 19848 Z= 0.333 Chirality : 0.045 0.190 2158 Planarity : 0.004 0.042 2390 Dihedral : 19.999 140.579 2894 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.11 % Rotamer: Outliers : 3.59 % Allowed : 12.09 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.16 (0.20), residues: 1672 helix: -0.16 (0.18), residues: 864 sheet: -2.68 (0.34), residues: 158 loop : -2.87 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 798 HIS 0.002 0.000 HIS B 593 PHE 0.017 0.002 PHE A 694 TYR 0.021 0.002 TYR D 844 ARG 0.009 0.001 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 8) link_NAG-ASN : angle 4.87505 ( 24) link_BETA1-4 : bond 0.00644 ( 8) link_BETA1-4 : angle 2.52643 ( 24) hydrogen bonds : bond 0.03551 ( 558) hydrogen bonds : angle 4.23163 ( 1620) SS BOND : bond 0.00619 ( 6) SS BOND : angle 1.37197 ( 12) link_BETA1-3 : bond 0.00457 ( 2) link_BETA1-3 : angle 3.04752 ( 6) covalent geometry : bond 0.00378 (14708) covalent geometry : angle 0.66785 (19782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7688 (t70) cc_final: 0.7335 (t0) REVERT: A 487 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7665 (mtmt) REVERT: A 566 TYR cc_start: 0.8307 (m-10) cc_final: 0.7818 (m-10) REVERT: A 703 ASP cc_start: 0.7269 (t70) cc_final: 0.6884 (t0) REVERT: A 715 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.7072 (p) REVERT: B 669 ASP cc_start: 0.8085 (t70) cc_final: 0.7677 (t70) REVERT: B 691 MET cc_start: 0.7678 (ttp) cc_final: 0.7434 (ttt) REVERT: B 743 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 825 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8156 (mt) REVERT: C 457 ASP cc_start: 0.7716 (t0) cc_final: 0.7455 (t0) REVERT: C 584 PHE cc_start: 0.6824 (t80) cc_final: 0.6547 (t80) REVERT: C 696 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7469 (mtmt) REVERT: C 719 LYS cc_start: 0.8337 (pptt) cc_final: 0.8046 (mtpp) REVERT: C 845 LYS cc_start: 0.7358 (tppt) cc_final: 0.6866 (tppp) REVERT: D 743 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: D 793 MET cc_start: 0.8450 (mmt) cc_final: 0.7640 (mtt) REVERT: D 819 ASN cc_start: 0.8353 (m110) cc_final: 0.8098 (m110) REVERT: D 825 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8141 (mt) outliers start: 52 outliers final: 27 residues processed: 192 average time/residue: 0.2662 time to fit residues: 75.0639 Evaluate side-chains 174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 754 GLN D 456 ASN D 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146972 restraints weight = 16270.041| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.29 r_work: 0.3409 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14732 Z= 0.194 Angle : 0.726 9.518 19848 Z= 0.347 Chirality : 0.046 0.212 2158 Planarity : 0.005 0.071 2390 Dihedral : 19.577 140.418 2894 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.78 % Favored : 91.87 % Rotamer: Outliers : 3.52 % Allowed : 12.78 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.95 (0.20), residues: 1672 helix: 0.06 (0.18), residues: 864 sheet: -2.73 (0.34), residues: 160 loop : -2.79 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 706 HIS 0.003 0.001 HIS D 593 PHE 0.018 0.002 PHE A 744 TYR 0.022 0.002 TYR D 844 ARG 0.011 0.001 ARG A 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 8) link_NAG-ASN : angle 5.06034 ( 24) link_BETA1-4 : bond 0.00557 ( 8) link_BETA1-4 : angle 2.54608 ( 24) hydrogen bonds : bond 0.03729 ( 558) hydrogen bonds : angle 4.20494 ( 1620) SS BOND : bond 0.00527 ( 6) SS BOND : angle 0.79819 ( 12) link_BETA1-3 : bond 0.00667 ( 2) link_BETA1-3 : angle 2.81490 ( 6) covalent geometry : bond 0.00478 (14708) covalent geometry : angle 0.69794 (19782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7682 (t70) cc_final: 0.7358 (t0) REVERT: A 566 TYR cc_start: 0.8446 (m-10) cc_final: 0.7931 (m-10) REVERT: A 703 ASP cc_start: 0.7403 (t70) cc_final: 0.7015 (t0) REVERT: B 669 ASP cc_start: 0.8374 (t70) cc_final: 0.8092 (t70) REVERT: B 677 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.5947 (mp10) REVERT: B 691 MET cc_start: 0.7791 (ttp) cc_final: 0.7525 (ttt) REVERT: B 793 MET cc_start: 0.8835 (tpt) cc_final: 0.8104 (mtt) REVERT: B 825 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8198 (mt) REVERT: C 584 PHE cc_start: 0.7069 (t80) cc_final: 0.6754 (t80) REVERT: C 661 VAL cc_start: 0.8508 (t) cc_final: 0.8216 (m) REVERT: C 696 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7571 (mtmt) REVERT: C 709 MET cc_start: 0.7389 (mtt) cc_final: 0.6716 (mtm) REVERT: C 719 LYS cc_start: 0.8326 (pptt) cc_final: 0.8062 (mtpp) REVERT: C 845 LYS cc_start: 0.7344 (tppt) cc_final: 0.6914 (tppp) REVERT: D 743 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: D 819 ASN cc_start: 0.8437 (m110) cc_final: 0.8118 (m110) REVERT: D 825 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8181 (mt) outliers start: 51 outliers final: 34 residues processed: 193 average time/residue: 0.2792 time to fit residues: 78.8262 Evaluate side-chains 182 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 160 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136955 restraints weight = 16664.933| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.70 r_work: 0.3318 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14732 Z= 0.148 Angle : 0.674 9.122 19848 Z= 0.321 Chirality : 0.044 0.184 2158 Planarity : 0.004 0.044 2390 Dihedral : 19.031 140.623 2894 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.66 % Favored : 92.05 % Rotamer: Outliers : 3.31 % Allowed : 13.40 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.54 (0.20), residues: 1672 helix: 0.42 (0.18), residues: 864 sheet: -2.46 (0.37), residues: 132 loop : -2.69 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 706 HIS 0.002 0.001 HIS B 593 PHE 0.012 0.001 PHE D 584 TYR 0.021 0.001 TYR B 844 ARG 0.006 0.000 ARG D 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 8) link_NAG-ASN : angle 4.93606 ( 24) link_BETA1-4 : bond 0.00618 ( 8) link_BETA1-4 : angle 2.48183 ( 24) hydrogen bonds : bond 0.03335 ( 558) hydrogen bonds : angle 4.06767 ( 1620) SS BOND : bond 0.00321 ( 6) SS BOND : angle 0.71900 ( 12) link_BETA1-3 : bond 0.00374 ( 2) link_BETA1-3 : angle 2.76996 ( 6) covalent geometry : bond 0.00359 (14708) covalent geometry : angle 0.64500 (19782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7745 (t70) cc_final: 0.7378 (t0) REVERT: A 566 TYR cc_start: 0.8563 (m-10) cc_final: 0.8073 (m-10) REVERT: A 703 ASP cc_start: 0.7539 (t70) cc_final: 0.7132 (t0) REVERT: A 706 TRP cc_start: 0.7854 (t-100) cc_final: 0.7590 (t-100) REVERT: A 715 SER cc_start: 0.7493 (OUTLIER) cc_final: 0.7102 (p) REVERT: B 677 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.5842 (mp10) REVERT: B 691 MET cc_start: 0.7853 (ttp) cc_final: 0.7566 (ttt) REVERT: B 793 MET cc_start: 0.8738 (tpt) cc_final: 0.7984 (mtt) REVERT: C 584 PHE cc_start: 0.7086 (t80) cc_final: 0.6791 (t80) REVERT: C 661 VAL cc_start: 0.8517 (t) cc_final: 0.8127 (m) REVERT: C 696 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7568 (mtmt) REVERT: C 719 LYS cc_start: 0.8447 (pptt) cc_final: 0.8072 (mtpp) REVERT: D 677 GLN cc_start: 0.6875 (mp10) cc_final: 0.6523 (mm-40) REVERT: D 743 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: D 819 ASN cc_start: 0.8528 (m110) cc_final: 0.8167 (m110) REVERT: D 825 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8159 (mt) outliers start: 48 outliers final: 33 residues processed: 185 average time/residue: 0.2891 time to fit residues: 79.3606 Evaluate side-chains 179 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 593 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138507 restraints weight = 16354.495| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.53 r_work: 0.3307 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14732 Z= 0.158 Angle : 0.685 8.977 19848 Z= 0.327 Chirality : 0.044 0.183 2158 Planarity : 0.004 0.043 2390 Dihedral : 18.691 140.583 2894 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.99 % Rotamer: Outliers : 3.59 % Allowed : 13.74 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.37 (0.21), residues: 1672 helix: 0.58 (0.18), residues: 864 sheet: -2.46 (0.37), residues: 132 loop : -2.62 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 706 HIS 0.002 0.001 HIS A 593 PHE 0.013 0.002 PHE D 584 TYR 0.025 0.002 TYR C 733 ARG 0.007 0.001 ARG D 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 8) link_NAG-ASN : angle 4.77411 ( 24) link_BETA1-4 : bond 0.00607 ( 8) link_BETA1-4 : angle 2.45483 ( 24) hydrogen bonds : bond 0.03346 ( 558) hydrogen bonds : angle 4.04258 ( 1620) SS BOND : bond 0.00318 ( 6) SS BOND : angle 0.64572 ( 12) link_BETA1-3 : bond 0.00324 ( 2) link_BETA1-3 : angle 2.62311 ( 6) covalent geometry : bond 0.00388 (14708) covalent geometry : angle 0.65794 (19782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7670 (t70) cc_final: 0.7327 (t0) REVERT: A 566 TYR cc_start: 0.8545 (m-10) cc_final: 0.8059 (m-10) REVERT: A 706 TRP cc_start: 0.7890 (t-100) cc_final: 0.7678 (t-100) REVERT: A 715 SER cc_start: 0.7532 (OUTLIER) cc_final: 0.7140 (p) REVERT: A 800 ARG cc_start: 0.8008 (tpm170) cc_final: 0.7622 (tpm170) REVERT: B 677 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.5844 (mp10) REVERT: B 682 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: B 691 MET cc_start: 0.7811 (ttp) cc_final: 0.7531 (ttt) REVERT: B 793 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7822 (mtt) REVERT: C 584 PHE cc_start: 0.7043 (t80) cc_final: 0.6762 (t80) REVERT: C 661 VAL cc_start: 0.8520 (t) cc_final: 0.8118 (m) REVERT: C 696 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7542 (mtmt) REVERT: C 719 LYS cc_start: 0.8435 (pptt) cc_final: 0.8071 (mtpp) REVERT: D 677 GLN cc_start: 0.6818 (mp10) cc_final: 0.6499 (mm-40) REVERT: D 743 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: D 819 ASN cc_start: 0.8525 (m110) cc_final: 0.8178 (m110) REVERT: D 825 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8150 (mt) outliers start: 52 outliers final: 36 residues processed: 180 average time/residue: 0.2693 time to fit residues: 71.0319 Evaluate side-chains 181 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136342 restraints weight = 16379.997| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.43 r_work: 0.3282 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14732 Z= 0.138 Angle : 0.664 8.819 19848 Z= 0.316 Chirality : 0.043 0.185 2158 Planarity : 0.004 0.044 2390 Dihedral : 18.285 140.534 2894 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.24 % Favored : 92.46 % Rotamer: Outliers : 3.25 % Allowed : 14.50 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.17 (0.21), residues: 1672 helix: 0.78 (0.18), residues: 864 sheet: -2.40 (0.38), residues: 132 loop : -2.57 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 798 HIS 0.001 0.000 HIS B 593 PHE 0.012 0.001 PHE B 584 TYR 0.022 0.001 TYR D 844 ARG 0.007 0.000 ARG A 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 8) link_NAG-ASN : angle 4.88461 ( 24) link_BETA1-4 : bond 0.00619 ( 8) link_BETA1-4 : angle 2.39115 ( 24) hydrogen bonds : bond 0.03196 ( 558) hydrogen bonds : angle 3.97258 ( 1620) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.62420 ( 12) link_BETA1-3 : bond 0.00282 ( 2) link_BETA1-3 : angle 2.63162 ( 6) covalent geometry : bond 0.00335 (14708) covalent geometry : angle 0.63599 (19782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7663 (t70) cc_final: 0.7333 (t0) REVERT: A 715 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7158 (p) REVERT: B 677 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.5715 (mp10) REVERT: B 682 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: B 691 MET cc_start: 0.7685 (ttp) cc_final: 0.7450 (ttt) REVERT: B 743 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: B 793 MET cc_start: 0.8588 (tpt) cc_final: 0.7816 (mtt) REVERT: C 584 PHE cc_start: 0.6972 (t80) cc_final: 0.6711 (t80) REVERT: C 661 VAL cc_start: 0.8523 (t) cc_final: 0.8127 (m) REVERT: C 691 MET cc_start: 0.7630 (ttp) cc_final: 0.7429 (ttp) REVERT: C 696 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7558 (mtmt) REVERT: C 719 LYS cc_start: 0.8391 (pptt) cc_final: 0.8046 (mtpp) REVERT: D 677 GLN cc_start: 0.6876 (mp10) cc_final: 0.6520 (mm-40) REVERT: D 743 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: D 825 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (mt) outliers start: 47 outliers final: 34 residues processed: 178 average time/residue: 0.2615 time to fit residues: 68.4759 Evaluate side-chains 182 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 126 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 35 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140286 restraints weight = 16125.538| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.50 r_work: 0.3328 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14732 Z= 0.153 Angle : 0.675 8.764 19848 Z= 0.321 Chirality : 0.043 0.188 2158 Planarity : 0.004 0.044 2390 Dihedral : 18.049 140.529 2894 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.60 % Favored : 92.05 % Rotamer: Outliers : 3.11 % Allowed : 14.57 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.14 (0.21), residues: 1672 helix: 0.86 (0.18), residues: 854 sheet: -2.39 (0.38), residues: 132 loop : -2.59 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 798 HIS 0.002 0.001 HIS A 792 PHE 0.013 0.001 PHE A 744 TYR 0.022 0.002 TYR D 844 ARG 0.006 0.000 ARG A 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 8) link_NAG-ASN : angle 4.79993 ( 24) link_BETA1-4 : bond 0.00585 ( 8) link_BETA1-4 : angle 2.39667 ( 24) hydrogen bonds : bond 0.03284 ( 558) hydrogen bonds : angle 3.97668 ( 1620) SS BOND : bond 0.00326 ( 6) SS BOND : angle 0.61692 ( 12) link_BETA1-3 : bond 0.00356 ( 2) link_BETA1-3 : angle 2.53060 ( 6) covalent geometry : bond 0.00374 (14708) covalent geometry : angle 0.64769 (19782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7597 (t70) cc_final: 0.7266 (t0) REVERT: A 715 SER cc_start: 0.7485 (OUTLIER) cc_final: 0.7155 (p) REVERT: A 800 ARG cc_start: 0.7970 (tpm170) cc_final: 0.7609 (tpm170) REVERT: B 677 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.5742 (mp10) REVERT: B 682 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7019 (m-10) REVERT: B 691 MET cc_start: 0.7825 (ttp) cc_final: 0.7547 (ttt) REVERT: B 743 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: B 793 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7953 (mtt) REVERT: C 584 PHE cc_start: 0.7052 (t80) cc_final: 0.6781 (t80) REVERT: C 691 MET cc_start: 0.7753 (ttp) cc_final: 0.7353 (ttm) REVERT: C 696 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7612 (mtmt) REVERT: C 709 MET cc_start: 0.7326 (mtm) cc_final: 0.6859 (mtm) REVERT: C 719 LYS cc_start: 0.8458 (pptt) cc_final: 0.8042 (mtpp) REVERT: D 677 GLN cc_start: 0.6877 (mp10) cc_final: 0.6524 (mm-40) REVERT: D 743 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: D 825 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8147 (mt) outliers start: 45 outliers final: 33 residues processed: 173 average time/residue: 0.2829 time to fit residues: 72.0263 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 147 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.0060 chunk 122 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136962 restraints weight = 16327.005| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.75 r_work: 0.3343 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14732 Z= 0.131 Angle : 0.655 9.156 19848 Z= 0.311 Chirality : 0.043 0.191 2158 Planarity : 0.004 0.045 2390 Dihedral : 17.730 140.482 2894 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.18 % Favored : 92.58 % Rotamer: Outliers : 2.56 % Allowed : 15.26 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.96 (0.21), residues: 1672 helix: 1.07 (0.19), residues: 846 sheet: -2.39 (0.38), residues: 132 loop : -2.54 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.001 0.000 HIS B 508 PHE 0.012 0.001 PHE D 584 TYR 0.022 0.001 TYR D 844 ARG 0.007 0.000 ARG A 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 8) link_NAG-ASN : angle 4.69779 ( 24) link_BETA1-4 : bond 0.00577 ( 8) link_BETA1-4 : angle 2.33236 ( 24) hydrogen bonds : bond 0.03120 ( 558) hydrogen bonds : angle 3.89700 ( 1620) SS BOND : bond 0.00317 ( 6) SS BOND : angle 0.58949 ( 12) link_BETA1-3 : bond 0.00383 ( 2) link_BETA1-3 : angle 2.55155 ( 6) covalent geometry : bond 0.00316 (14708) covalent geometry : angle 0.62864 (19782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7458 (t70) cc_final: 0.7179 (t0) REVERT: A 706 TRP cc_start: 0.7958 (t-100) cc_final: 0.7311 (t-100) REVERT: A 715 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.7151 (p) REVERT: A 800 ARG cc_start: 0.7870 (tpm170) cc_final: 0.7165 (ptp-110) REVERT: B 677 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: B 682 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: B 691 MET cc_start: 0.7674 (ttp) cc_final: 0.7446 (ttt) REVERT: B 743 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: B 793 MET cc_start: 0.8534 (tpt) cc_final: 0.7808 (mtt) REVERT: C 553 PHE cc_start: 0.8888 (m-10) cc_final: 0.8674 (m-80) REVERT: C 584 PHE cc_start: 0.6933 (t80) cc_final: 0.6680 (t80) REVERT: C 696 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7514 (mtmt) REVERT: C 709 MET cc_start: 0.7259 (mtm) cc_final: 0.6830 (mtm) REVERT: C 719 LYS cc_start: 0.8393 (pptt) cc_final: 0.8039 (mtpp) REVERT: C 723 GLU cc_start: 0.6752 (tp30) cc_final: 0.6428 (tp30) REVERT: D 677 GLN cc_start: 0.6884 (mp10) cc_final: 0.6520 (mm-40) REVERT: D 743 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: D 825 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8091 (mt) outliers start: 37 outliers final: 29 residues processed: 172 average time/residue: 0.2744 time to fit residues: 69.4202 Evaluate side-chains 173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 58 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 HIS B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135534 restraints weight = 16382.651| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.55 r_work: 0.3269 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14732 Z= 0.146 Angle : 0.680 9.429 19848 Z= 0.325 Chirality : 0.043 0.191 2158 Planarity : 0.004 0.045 2390 Dihedral : 17.623 140.643 2894 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.24 % Favored : 92.40 % Rotamer: Outliers : 2.83 % Allowed : 15.26 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.98 (0.21), residues: 1672 helix: 1.02 (0.18), residues: 852 sheet: -2.30 (0.39), residues: 130 loop : -2.57 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.002 0.001 HIS B 593 PHE 0.012 0.001 PHE A 744 TYR 0.023 0.002 TYR D 844 ARG 0.007 0.000 ARG A 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 8) link_NAG-ASN : angle 4.68600 ( 24) link_BETA1-4 : bond 0.00568 ( 8) link_BETA1-4 : angle 2.35126 ( 24) hydrogen bonds : bond 0.03188 ( 558) hydrogen bonds : angle 3.89652 ( 1620) SS BOND : bond 0.00369 ( 6) SS BOND : angle 0.98594 ( 12) link_BETA1-3 : bond 0.00387 ( 2) link_BETA1-3 : angle 2.48011 ( 6) covalent geometry : bond 0.00354 (14708) covalent geometry : angle 0.65386 (19782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7332.67 seconds wall clock time: 127 minutes 47.10 seconds (7667.10 seconds total)