Starting phenix.real_space_refine on Sat Aug 23 21:50:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fws_29517/08_2025/8fws_29517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fws_29517/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fws_29517/08_2025/8fws_29517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fws_29517/08_2025/8fws_29517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fws_29517/08_2025/8fws_29517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fws_29517/08_2025/8fws_29517.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.83, per 1000 atoms: 0.27 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: 1.31 Conformation dependent library (CDL) restraints added in 602.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.48 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: 2.45 Time building geometry restraints manager: 1.71 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: 3.950 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG B 713 TYR 0.028 0.003 TYR B 702 PHE 0.029 0.003 PHE D 446 TRP 0.019 0.003 TRP D 706 HIS 0.005 0.001 HIS D 593 Details of bonding type rmsd covalent geometry : bond 0.01180 (14708) covalent geometry : angle 1.61966 (19782) SS BOND : bond 0.01844 ( 6) SS BOND : angle 1.36329 ( 12) hydrogen bonds : bond 0.30928 ( 558) hydrogen bonds : angle 11.22768 ( 1620) link_BETA1-3 : bond 0.00161 ( 2) link_BETA1-3 : angle 3.28805 ( 6) link_BETA1-4 : bond 0.01669 ( 8) link_BETA1-4 : angle 4.06420 ( 24) link_NAG-ASN : bond 0.01837 ( 8) link_NAG-ASN : angle 7.93277 ( 24) *********************** 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 : 0.567 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: 0.1557 time to fit residues: 78.0008 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 : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.176641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147229 restraints weight = 16066.700| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.97 r_work: 0.3397 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2417 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= 0.178 Angle : 0.792 9.568 19848 Z= 0.388 Chirality : 0.047 0.159 2158 Planarity : 0.006 0.048 2390 Dihedral : 22.735 139.037 2894 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.95 % Favored : 91.57 % Rotamer: Outliers : 2.07 % Allowed : 10.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.07 (0.17), residues: 1672 helix: -2.19 (0.14), residues: 842 sheet: -3.14 (0.34), residues: 152 loop : -3.13 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 713 TYR 0.022 0.002 TYR D 702 PHE 0.016 0.002 PHE B 735 TRP 0.016 0.002 TRP C 706 HIS 0.003 0.001 HIS D 593 Details of bonding type rmsd covalent geometry : bond 0.00417 (14708) covalent geometry : angle 0.75998 (19782) SS BOND : bond 0.00714 ( 6) SS BOND : angle 1.53494 ( 12) hydrogen bonds : bond 0.04868 ( 558) hydrogen bonds : angle 5.12752 ( 1620) link_BETA1-3 : bond 0.00671 ( 2) link_BETA1-3 : angle 3.82125 ( 6) link_BETA1-4 : bond 0.00797 ( 8) link_BETA1-4 : angle 2.68288 ( 24) link_NAG-ASN : bond 0.00670 ( 8) link_NAG-ASN : angle 5.53292 ( 24) *********************** 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 228 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.558 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: 0.8247 (m-10) cc_final: 0.7801 (m-10) REVERT: A 691 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6835 (ttt) REVERT: A 715 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7177 (p) REVERT: A 719 LYS cc_start: 0.7924 (pptt) cc_final: 0.7674 (mtpp) REVERT: B 691 MET cc_start: 0.7715 (ttp) cc_final: 0.7435 (ttt) REVERT: B 790 LYS cc_start: 0.7812 (mptp) cc_final: 0.7487 (mmmt) REVERT: B 825 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8168 (mt) REVERT: C 584 PHE cc_start: 0.6835 (t80) cc_final: 0.6604 (t80) REVERT: C 696 LYS cc_start: 0.7707 (mtpt) cc_final: 0.7431 (mtmt) REVERT: C 719 LYS cc_start: 0.8254 (pptt) cc_final: 0.8052 (mtpp) REVERT: D 691 MET cc_start: 0.7653 (tmm) cc_final: 0.7443 (ttt) REVERT: D 790 LYS cc_start: 0.7654 (mptp) cc_final: 0.7238 (mmmt) REVERT: D 819 ASN cc_start: 0.8260 (m110) cc_final: 0.7997 (m-40) REVERT: D 825 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8200 (mt) outliers start: 30 outliers final: 17 residues processed: 215 average time/residue: 0.1338 time to fit residues: 42.1863 Evaluate side-chains 175 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 697 SER 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 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN A 747 GLN B 456 ASN D 456 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147723 restraints weight = 15932.053| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.80 r_work: 0.3327 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3008 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= 0.161 Angle : 0.728 10.696 19848 Z= 0.350 Chirality : 0.045 0.171 2158 Planarity : 0.004 0.043 2390 Dihedral : 21.115 140.405 2894 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.60 % Favored : 91.93 % Rotamer: Outliers : 2.56 % Allowed : 11.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (0.19), residues: 1672 helix: -0.84 (0.17), residues: 852 sheet: -2.84 (0.34), residues: 154 loop : -2.93 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 712 TYR 0.020 0.002 TYR A 590 PHE 0.019 0.002 PHE D 579 TRP 0.015 0.001 TRP D 798 HIS 0.003 0.000 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00383 (14708) covalent geometry : angle 0.69738 (19782) SS BOND : bond 0.00489 ( 6) SS BOND : angle 1.85742 ( 12) hydrogen bonds : bond 0.03972 ( 558) hydrogen bonds : angle 4.46582 ( 1620) link_BETA1-3 : bond 0.00536 ( 2) link_BETA1-3 : angle 3.44694 ( 6) link_BETA1-4 : bond 0.00784 ( 8) link_BETA1-4 : angle 2.66497 ( 24) link_NAG-ASN : bond 0.00634 ( 8) link_NAG-ASN : angle 5.05711 ( 24) *********************** 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 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7725 (t70) cc_final: 0.7321 (t0) REVERT: A 566 TYR cc_start: 0.8388 (m-10) cc_final: 0.7867 (m-10) REVERT: A 664 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7973 (mtt) REVERT: A 703 ASP cc_start: 0.7338 (t70) cc_final: 0.6913 (t0) REVERT: A 715 SER cc_start: 0.7453 (OUTLIER) cc_final: 0.7037 (p) REVERT: B 677 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.5874 (mp10) REVERT: B 691 MET cc_start: 0.7817 (ttp) cc_final: 0.7507 (ttt) REVERT: B 790 LYS cc_start: 0.7940 (mptp) cc_final: 0.7549 (tptt) REVERT: B 825 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8126 (mt) REVERT: C 584 PHE cc_start: 0.6847 (t80) cc_final: 0.6607 (t80) REVERT: C 661 VAL cc_start: 0.8541 (t) cc_final: 0.8260 (m) REVERT: C 696 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7431 (mtmt) REVERT: C 719 LYS cc_start: 0.8368 (pptt) cc_final: 0.8089 (mtpp) REVERT: C 845 LYS cc_start: 0.7237 (tppt) cc_final: 0.6716 (tppp) REVERT: D 743 GLU cc_start: 0.8371 (mp0) cc_final: 0.7981 (mp0) REVERT: D 790 LYS cc_start: 0.7713 (mptp) cc_final: 0.7287 (tptt) REVERT: D 819 ASN cc_start: 0.8472 (m110) cc_final: 0.8118 (m-40) REVERT: D 825 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8182 (mt) outliers start: 37 outliers final: 23 residues processed: 182 average time/residue: 0.1307 time to fit residues: 34.8596 Evaluate side-chains 168 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 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 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 110 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.164228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133334 restraints weight = 16600.734| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.69 r_work: 0.3288 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14732 Z= 0.166 Angle : 0.703 9.748 19848 Z= 0.337 Chirality : 0.045 0.215 2158 Planarity : 0.004 0.042 2390 Dihedral : 20.041 140.492 2894 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.36 % Favored : 92.28 % Rotamer: Outliers : 3.66 % Allowed : 12.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.20), residues: 1672 helix: -0.17 (0.18), residues: 864 sheet: -2.64 (0.34), residues: 158 loop : -2.88 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 712 TYR 0.020 0.002 TYR D 844 PHE 0.017 0.002 PHE D 584 TRP 0.011 0.001 TRP A 706 HIS 0.002 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00399 (14708) covalent geometry : angle 0.67430 (19782) SS BOND : bond 0.00616 ( 6) SS BOND : angle 1.06404 ( 12) hydrogen bonds : bond 0.03596 ( 558) hydrogen bonds : angle 4.24308 ( 1620) link_BETA1-3 : bond 0.00342 ( 2) link_BETA1-3 : angle 3.00405 ( 6) link_BETA1-4 : bond 0.00766 ( 8) link_BETA1-4 : angle 2.55441 ( 24) link_NAG-ASN : bond 0.00559 ( 8) link_NAG-ASN : angle 5.01349 ( 24) *********************** 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 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7694 (t70) cc_final: 0.7338 (t0) REVERT: A 487 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7625 (mtmt) REVERT: A 566 TYR cc_start: 0.8373 (m-10) cc_final: 0.7852 (m-10) REVERT: A 664 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: A 674 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8129 (tp) REVERT: A 703 ASP cc_start: 0.7414 (t70) cc_final: 0.7022 (t0) REVERT: A 715 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7014 (p) REVERT: B 669 ASP cc_start: 0.8112 (t70) cc_final: 0.7701 (t70) REVERT: B 691 MET cc_start: 0.7720 (ttp) cc_final: 0.7474 (ttt) REVERT: B 743 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: B 825 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8173 (mt) REVERT: C 457 ASP cc_start: 0.7609 (t0) cc_final: 0.7278 (t0) REVERT: C 584 PHE cc_start: 0.6894 (t80) cc_final: 0.6619 (t80) REVERT: C 696 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7482 (mtmt) REVERT: C 719 LYS cc_start: 0.8339 (pptt) cc_final: 0.8049 (mtpp) REVERT: C 845 LYS cc_start: 0.7379 (tppt) cc_final: 0.6869 (tppp) REVERT: D 743 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: D 790 LYS cc_start: 0.7737 (mptp) cc_final: 0.7533 (tptt) REVERT: D 793 MET cc_start: 0.8435 (mmt) cc_final: 0.7611 (mtt) REVERT: D 819 ASN cc_start: 0.8396 (m110) cc_final: 0.8121 (m110) REVERT: D 825 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8161 (mt) outliers start: 53 outliers final: 30 residues processed: 192 average time/residue: 0.1310 time to fit residues: 37.1879 Evaluate side-chains 173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 664 MET Chi-restraints excluded: chain A residue 674 LEU 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 556 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.176322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149940 restraints weight = 16143.335| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.81 r_work: 0.3400 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 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 = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14732 Z= 0.121 Angle : 0.655 9.286 19848 Z= 0.312 Chirality : 0.043 0.187 2158 Planarity : 0.004 0.049 2390 Dihedral : 19.257 140.532 2894 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 3.11 % Allowed : 12.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.20), residues: 1672 helix: 0.36 (0.18), residues: 864 sheet: -2.35 (0.36), residues: 132 loop : -2.74 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 712 TYR 0.020 0.001 TYR D 844 PHE 0.013 0.001 PHE B 612 TRP 0.010 0.001 TRP D 798 HIS 0.002 0.001 HIS D 593 Details of bonding type rmsd covalent geometry : bond 0.00280 (14708) covalent geometry : angle 0.62757 (19782) SS BOND : bond 0.00429 ( 6) SS BOND : angle 0.81835 ( 12) hydrogen bonds : bond 0.03168 ( 558) hydrogen bonds : angle 4.02167 ( 1620) link_BETA1-3 : bond 0.00312 ( 2) link_BETA1-3 : angle 2.96790 ( 6) link_BETA1-4 : bond 0.00647 ( 8) link_BETA1-4 : angle 2.44139 ( 24) link_NAG-ASN : bond 0.00766 ( 8) link_NAG-ASN : angle 4.66141 ( 24) *********************** 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 192 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7705 (t70) cc_final: 0.7321 (t0) REVERT: A 566 TYR cc_start: 0.8471 (m-10) cc_final: 0.7960 (m-10) REVERT: A 664 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8221 (mtt) REVERT: A 674 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8105 (tp) REVERT: A 703 ASP cc_start: 0.7403 (t70) cc_final: 0.7001 (t0) REVERT: B 669 ASP cc_start: 0.8372 (t70) cc_final: 0.8076 (t70) REVERT: B 677 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.5985 (mp10) REVERT: B 691 MET cc_start: 0.7810 (ttp) cc_final: 0.7538 (ttt) REVERT: B 743 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: B 793 MET cc_start: 0.8900 (tpt) cc_final: 0.8096 (mtt) REVERT: C 584 PHE cc_start: 0.6952 (t80) cc_final: 0.6656 (t80) REVERT: C 661 VAL cc_start: 0.8451 (t) cc_final: 0.8157 (m) REVERT: C 696 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7528 (mtmt) REVERT: C 709 MET cc_start: 0.7303 (mtm) cc_final: 0.6745 (mtm) REVERT: C 719 LYS cc_start: 0.8386 (pptt) cc_final: 0.8095 (mtpp) REVERT: C 845 LYS cc_start: 0.7326 (tppt) cc_final: 0.6875 (tppp) REVERT: D 677 GLN cc_start: 0.6913 (mp10) cc_final: 0.6568 (mm-40) REVERT: D 743 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: D 790 LYS cc_start: 0.7851 (mptp) cc_final: 0.7627 (tptt) REVERT: D 793 MET cc_start: 0.8610 (mmt) cc_final: 0.7740 (mtt) REVERT: D 819 ASN cc_start: 0.8429 (m110) cc_final: 0.8119 (m110) REVERT: D 825 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8139 (mt) outliers start: 45 outliers final: 25 residues processed: 177 average time/residue: 0.1380 time to fit residues: 35.7892 Evaluate side-chains 173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 664 MET Chi-restraints excluded: chain A residue 674 LEU 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 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 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 705 MET Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 92 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136758 restraints weight = 16419.196| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.74 r_work: 0.3284 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14732 Z= 0.133 Angle : 0.658 9.821 19848 Z= 0.313 Chirality : 0.043 0.174 2158 Planarity : 0.004 0.042 2390 Dihedral : 18.774 140.668 2894 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.42 % Favored : 92.22 % Rotamer: Outliers : 2.90 % Allowed : 13.12 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.21), residues: 1672 helix: 0.63 (0.18), residues: 864 sheet: -2.29 (0.37), residues: 130 loop : -2.64 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 748 TYR 0.022 0.001 TYR D 844 PHE 0.013 0.001 PHE D 584 TRP 0.009 0.001 TRP A 706 HIS 0.001 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00317 (14708) covalent geometry : angle 0.63074 (19782) SS BOND : bond 0.00340 ( 6) SS BOND : angle 0.68110 ( 12) hydrogen bonds : bond 0.03227 ( 558) hydrogen bonds : angle 3.93174 ( 1620) link_BETA1-3 : bond 0.00303 ( 2) link_BETA1-3 : angle 2.82803 ( 6) link_BETA1-4 : bond 0.00607 ( 8) link_BETA1-4 : angle 2.39509 ( 24) link_NAG-ASN : bond 0.00626 ( 8) link_NAG-ASN : angle 4.67698 ( 24) *********************** 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 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7699 (t70) cc_final: 0.7357 (t0) REVERT: A 566 TYR cc_start: 0.8350 (m-10) cc_final: 0.7853 (m-10) REVERT: A 664 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: A 703 ASP cc_start: 0.7338 (t70) cc_final: 0.6929 (t0) REVERT: A 715 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7018 (p) REVERT: B 677 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.5898 (mp10) REVERT: B 691 MET cc_start: 0.7656 (ttp) cc_final: 0.7424 (ttt) REVERT: B 743 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 793 MET cc_start: 0.8719 (tpt) cc_final: 0.7876 (mtt) REVERT: C 584 PHE cc_start: 0.6989 (t80) cc_final: 0.6729 (t80) REVERT: C 661 VAL cc_start: 0.8519 (t) cc_final: 0.8204 (m) REVERT: C 696 LYS cc_start: 0.7775 (mtpt) cc_final: 0.7465 (mtmt) REVERT: C 709 MET cc_start: 0.7208 (mtm) cc_final: 0.6598 (mtm) REVERT: C 719 LYS cc_start: 0.8305 (pptt) cc_final: 0.8049 (mtpp) REVERT: C 845 LYS cc_start: 0.7242 (tppt) cc_final: 0.6865 (tppp) REVERT: D 677 GLN cc_start: 0.6835 (mp10) cc_final: 0.6513 (mm-40) REVERT: D 743 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: D 793 MET cc_start: 0.8425 (mmt) cc_final: 0.7635 (mtt) REVERT: D 819 ASN cc_start: 0.8369 (m110) cc_final: 0.8081 (m110) REVERT: D 825 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8119 (mt) outliers start: 42 outliers final: 29 residues processed: 181 average time/residue: 0.1189 time to fit residues: 31.8676 Evaluate side-chains 176 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 568 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 705 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 754 GLN D 593 HIS D 596 ASN D 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.175238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.150456 restraints weight = 15923.513| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.66 r_work: 0.3413 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14732 Z= 0.143 Angle : 0.660 9.137 19848 Z= 0.315 Chirality : 0.043 0.180 2158 Planarity : 0.004 0.043 2390 Dihedral : 18.458 140.530 2894 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.11 % Rotamer: Outliers : 2.83 % Allowed : 13.74 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1672 helix: 0.83 (0.18), residues: 852 sheet: -2.34 (0.37), residues: 132 loop : -2.59 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 712 TYR 0.025 0.001 TYR A 542 PHE 0.013 0.001 PHE D 584 TRP 0.023 0.001 TRP D 798 HIS 0.001 0.000 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00347 (14708) covalent geometry : angle 0.63464 (19782) SS BOND : bond 0.00319 ( 6) SS BOND : angle 0.60073 ( 12) hydrogen bonds : bond 0.03276 ( 558) hydrogen bonds : angle 3.95897 ( 1620) link_BETA1-3 : bond 0.00300 ( 2) link_BETA1-3 : angle 2.69784 ( 6) link_BETA1-4 : bond 0.00599 ( 8) link_BETA1-4 : angle 2.38723 ( 24) link_NAG-ASN : bond 0.00601 ( 8) link_NAG-ASN : angle 4.58442 ( 24) *********************** 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 185 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7643 (t70) cc_final: 0.7317 (t0) REVERT: A 566 TYR cc_start: 0.8440 (m-10) cc_final: 0.7927 (m-10) REVERT: A 664 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8086 (mtt) REVERT: A 706 TRP cc_start: 0.7865 (t-100) cc_final: 0.7635 (t-100) REVERT: A 715 SER cc_start: 0.7451 (OUTLIER) cc_final: 0.7065 (p) REVERT: B 677 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.5928 (mp10) REVERT: B 691 MET cc_start: 0.7738 (ttp) cc_final: 0.7484 (ttt) REVERT: B 743 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 793 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7915 (mtt) REVERT: C 584 PHE cc_start: 0.7027 (t80) cc_final: 0.6759 (t80) REVERT: C 661 VAL cc_start: 0.8484 (t) cc_final: 0.8093 (m) REVERT: C 696 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7500 (mtmt) REVERT: C 709 MET cc_start: 0.7261 (mtm) cc_final: 0.6736 (mtm) REVERT: C 719 LYS cc_start: 0.8391 (pptt) cc_final: 0.8077 (mtpp) REVERT: C 723 GLU cc_start: 0.6847 (tp30) cc_final: 0.6499 (tp30) REVERT: C 845 LYS cc_start: 0.7266 (tppt) cc_final: 0.6886 (tppp) REVERT: D 677 GLN cc_start: 0.6946 (mp10) cc_final: 0.6553 (mm-40) REVERT: D 743 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: D 793 MET cc_start: 0.8517 (mmt) cc_final: 0.7643 (mtt) REVERT: D 825 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8148 (mt) outliers start: 41 outliers final: 29 residues processed: 170 average time/residue: 0.1316 time to fit residues: 32.8265 Evaluate side-chains 175 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 568 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 743 GLU Chi-restraints excluded: chain B residue 793 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 0.0270 chunk 157 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 134 optimal weight: 0.2980 chunk 146 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.173071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147026 restraints weight = 16130.994| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.26 r_work: 0.3408 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14732 Z= 0.107 Angle : 0.630 9.656 19848 Z= 0.299 Chirality : 0.041 0.202 2158 Planarity : 0.004 0.044 2390 Dihedral : 17.876 140.590 2894 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.82 % Favored : 92.94 % Rotamer: Outliers : 2.56 % Allowed : 14.09 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.21), residues: 1672 helix: 1.18 (0.19), residues: 852 sheet: -2.30 (0.38), residues: 132 loop : -2.54 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 748 TYR 0.021 0.001 TYR D 844 PHE 0.010 0.001 PHE D 584 TRP 0.015 0.001 TRP D 798 HIS 0.001 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00243 (14708) covalent geometry : angle 0.59882 (19782) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.59378 ( 12) hydrogen bonds : bond 0.02970 ( 558) hydrogen bonds : angle 3.79264 ( 1620) link_BETA1-3 : bond 0.00269 ( 2) link_BETA1-3 : angle 2.72056 ( 6) link_BETA1-4 : bond 0.00640 ( 8) link_BETA1-4 : angle 2.26215 ( 24) link_NAG-ASN : bond 0.00949 ( 8) link_NAG-ASN : angle 5.05847 ( 24) *********************** 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 188 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7605 (t70) cc_final: 0.7280 (t0) REVERT: A 664 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: A 715 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.7083 (p) REVERT: A 800 ARG cc_start: 0.7983 (tpm170) cc_final: 0.7601 (tpm170) REVERT: B 677 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.5979 (mp10) REVERT: B 691 MET cc_start: 0.7703 (ttp) cc_final: 0.7443 (ttt) REVERT: B 743 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 793 MET cc_start: 0.8807 (tpt) cc_final: 0.7989 (mtt) REVERT: C 584 PHE cc_start: 0.6973 (t80) cc_final: 0.6714 (t80) REVERT: C 661 VAL cc_start: 0.8479 (t) cc_final: 0.8091 (m) REVERT: C 696 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7462 (mtmt) REVERT: C 705 MET cc_start: 0.8970 (mtp) cc_final: 0.8719 (mtp) REVERT: C 709 MET cc_start: 0.7187 (mtm) cc_final: 0.6737 (mtm) REVERT: C 719 LYS cc_start: 0.8427 (pptt) cc_final: 0.8089 (mtpp) REVERT: C 845 LYS cc_start: 0.7220 (tppt) cc_final: 0.6837 (tppp) REVERT: D 677 GLN cc_start: 0.6941 (mp10) cc_final: 0.6560 (mm-40) REVERT: D 743 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: D 793 MET cc_start: 0.8451 (mmt) cc_final: 0.7588 (mtt) outliers start: 37 outliers final: 22 residues processed: 176 average time/residue: 0.1313 time to fit residues: 34.0090 Evaluate side-chains 169 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 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 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 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 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 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 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.171351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142473 restraints weight = 16205.551| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.59 r_work: 0.3356 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14732 Z= 0.158 Angle : 0.683 8.855 19848 Z= 0.325 Chirality : 0.044 0.186 2158 Planarity : 0.004 0.043 2390 Dihedral : 17.805 140.694 2894 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.11 % Rotamer: Outliers : 2.35 % Allowed : 14.92 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.21), residues: 1672 helix: 1.08 (0.18), residues: 854 sheet: -2.34 (0.38), residues: 132 loop : -2.54 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 663 TYR 0.023 0.002 TYR D 844 PHE 0.014 0.002 PHE D 533 TRP 0.017 0.001 TRP D 798 HIS 0.002 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00387 (14708) covalent geometry : angle 0.65410 (19782) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.56558 ( 12) hydrogen bonds : bond 0.03328 ( 558) hydrogen bonds : angle 3.89585 ( 1620) link_BETA1-3 : bond 0.00431 ( 2) link_BETA1-3 : angle 2.47699 ( 6) link_BETA1-4 : bond 0.00496 ( 8) link_BETA1-4 : angle 2.39549 ( 24) link_NAG-ASN : bond 0.00649 ( 8) link_NAG-ASN : angle 5.08507 ( 24) *********************** 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 181 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7461 (t70) cc_final: 0.7159 (t0) REVERT: A 664 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8145 (mtt) REVERT: A 715 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7079 (p) REVERT: B 507 ASP cc_start: 0.7419 (m-30) cc_final: 0.7160 (m-30) REVERT: B 677 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.5836 (mp10) REVERT: B 691 MET cc_start: 0.7814 (ttp) cc_final: 0.7569 (ttt) REVERT: B 793 MET cc_start: 0.8675 (tpt) cc_final: 0.7880 (mtt) REVERT: C 584 PHE cc_start: 0.7037 (t80) cc_final: 0.6754 (t80) REVERT: C 696 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7549 (mtmt) REVERT: C 705 MET cc_start: 0.8996 (mtp) cc_final: 0.8774 (mtp) REVERT: C 709 MET cc_start: 0.7241 (mtm) cc_final: 0.6784 (mtm) REVERT: C 719 LYS cc_start: 0.8465 (pptt) cc_final: 0.8103 (mtpp) REVERT: D 677 GLN cc_start: 0.6900 (mp10) cc_final: 0.6547 (mm-40) REVERT: D 743 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7944 (mt-10) outliers start: 34 outliers final: 24 residues processed: 168 average time/residue: 0.1375 time to fit residues: 33.6852 Evaluate side-chains 169 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 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 820 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 539 SER 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 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 6.9990 chunk 79 optimal weight: 0.0470 chunk 148 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 157 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.175676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148284 restraints weight = 15932.158| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.57 r_work: 0.3399 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14732 Z= 0.145 Angle : 0.671 9.083 19848 Z= 0.319 Chirality : 0.043 0.192 2158 Planarity : 0.004 0.043 2390 Dihedral : 17.686 140.505 2894 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.30 % Favored : 92.40 % Rotamer: Outliers : 2.28 % Allowed : 15.33 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.21), residues: 1672 helix: 1.15 (0.18), residues: 852 sheet: -2.34 (0.38), residues: 130 loop : -2.55 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 775 TYR 0.022 0.001 TYR D 844 PHE 0.013 0.001 PHE D 584 TRP 0.015 0.001 TRP D 798 HIS 0.001 0.000 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00352 (14708) covalent geometry : angle 0.64159 (19782) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.51312 ( 12) hydrogen bonds : bond 0.03208 ( 558) hydrogen bonds : angle 3.87870 ( 1620) link_BETA1-3 : bond 0.00368 ( 2) link_BETA1-3 : angle 2.50766 ( 6) link_BETA1-4 : bond 0.00576 ( 8) link_BETA1-4 : angle 2.37464 ( 24) link_NAG-ASN : bond 0.00681 ( 8) link_NAG-ASN : angle 5.04553 ( 24) ********************** 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 176 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7437 (t70) cc_final: 0.7166 (t0) REVERT: A 715 SER cc_start: 0.7390 (OUTLIER) cc_final: 0.7088 (p) REVERT: B 677 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.5810 (mp10) REVERT: B 691 MET cc_start: 0.7733 (ttp) cc_final: 0.7495 (ttt) REVERT: B 793 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7936 (mtt) REVERT: C 584 PHE cc_start: 0.6997 (t80) cc_final: 0.6725 (t80) REVERT: C 696 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7562 (mtmt) REVERT: C 709 MET cc_start: 0.7245 (mtm) cc_final: 0.6868 (mtm) REVERT: C 719 LYS cc_start: 0.8382 (pptt) cc_final: 0.8123 (mtpp) REVERT: D 677 GLN cc_start: 0.6918 (mp10) cc_final: 0.6563 (mm-40) REVERT: D 743 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7837 (mt-10) outliers start: 33 outliers final: 26 residues processed: 164 average time/residue: 0.1319 time to fit residues: 31.9660 Evaluate side-chains 167 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 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 793 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.173108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144985 restraints weight = 16058.133| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.53 r_work: 0.3353 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14732 Z= 0.142 Angle : 0.675 9.658 19848 Z= 0.322 Chirality : 0.043 0.192 2158 Planarity : 0.004 0.043 2390 Dihedral : 17.505 140.514 2894 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.42 % Favored : 92.28 % Rotamer: Outliers : 2.35 % Allowed : 15.26 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.21), residues: 1672 helix: 1.19 (0.18), residues: 852 sheet: -2.32 (0.38), residues: 130 loop : -2.51 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 748 TYR 0.022 0.001 TYR D 844 PHE 0.011 0.001 PHE D 533 TRP 0.015 0.001 TRP D 798 HIS 0.001 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00346 (14708) covalent geometry : angle 0.64622 (19782) SS BOND : bond 0.00384 ( 6) SS BOND : angle 0.81155 ( 12) hydrogen bonds : bond 0.03186 ( 558) hydrogen bonds : angle 3.87183 ( 1620) link_BETA1-3 : bond 0.00385 ( 2) link_BETA1-3 : angle 2.48420 ( 6) link_BETA1-4 : bond 0.00568 ( 8) link_BETA1-4 : angle 2.34771 ( 24) link_NAG-ASN : bond 0.00662 ( 8) link_NAG-ASN : angle 4.98065 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.80 seconds wall clock time: 68 minutes 15.89 seconds (4095.89 seconds total)