Starting phenix.real_space_refine on Tue Dec 31 05:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fws_29517/12_2024/8fws_29517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fws_29517/12_2024/8fws_29517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fws_29517/12_2024/8fws_29517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fws_29517/12_2024/8fws_29517.map" model { file = "/net/cci-nas-00/data/ceres_data/8fws_29517/12_2024/8fws_29517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fws_29517/12_2024/8fws_29517.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 16 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 6 4.78 5 C 9432 2.51 5 N 2190 2.21 5 O 2686 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14416 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 362 Unusual residues: {' CL': 1, ' NA': 3, '2J9': 2, 'NAG': 1, 'POV': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 256 Unusual residues: {' CL': 1, ' NA': 1, '2J9': 2, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {' NA': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.23, per 1000 atoms: 0.64 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: 4.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 18 sheets defined 49.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.946A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.021A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.696A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.516A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 631 through 665 removed outlier: 3.575A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.039A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.688A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.710A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.903A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.605A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.538A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.517A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.680A pdb=" N ASN B 557 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.729A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.618A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.570A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.648A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 711 removed outlier: 3.590A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.553A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.704A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.856A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.731A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 845 " --> pdb=" O GLU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.946A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 4.022A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.695A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.516A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 631 through 665 removed outlier: 3.576A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 removed outlier: 4.040A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.688A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 712 Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 748 removed outlier: 3.710A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.902A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.604A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 799 Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.538A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.518A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.679A pdb=" N ASN D 557 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.729A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.618A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.569A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.648A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 711 removed outlier: 3.590A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.553A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.703A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 789 removed outlier: 3.857A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 794 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.731A pdb=" N VAL D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 845 " --> pdb=" O GLU D 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.163A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 683 removed outlier: 7.194A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.558A pdb=" N GLU B 460 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.247A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.163A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.830A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 681 through 683 removed outlier: 7.194A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 445 through 446 removed outlier: 3.558A pdb=" N GLU D 460 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB8, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.058A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.248A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 4.54 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: 3.660 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 33.500 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- 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 14708 Z= 0.681 Angle : 1.620 32.889 19782 Z= 0.770 Chirality : 0.116 2.318 2158 Planarity : 0.007 0.058 2390 Dihedral : 19.895 143.040 6034 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.49 % Favored : 91.15 % Rotamer: Outliers : 0.55 % Allowed : 4.28 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.96 (0.13), residues: 1672 helix: -4.37 (0.07), residues: 802 sheet: -3.11 (0.38), residues: 134 loop : -3.49 (0.17), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 706 HIS 0.005 0.001 HIS D 593 PHE 0.029 0.003 PHE D 446 TYR 0.028 0.003 TYR B 702 ARG 0.008 0.001 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 356 time to evaluate : 1.408 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: 0.3199 time to fit residues: 159.6709 Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 591 ASN A 596 ASN A 604 ASN B 456 ASN B 621 GLN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 621 GLN D 456 ASN D 604 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14708 Z= 0.271 Angle : 0.762 9.623 19782 Z= 0.382 Chirality : 0.047 0.171 2158 Planarity : 0.006 0.048 2390 Dihedral : 22.729 139.542 2894 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.13 % Favored : 91.39 % Rotamer: Outliers : 2.14 % Allowed : 10.15 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.16), residues: 1672 helix: -2.26 (0.14), residues: 846 sheet: -3.03 (0.33), residues: 158 loop : -3.12 (0.20), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 706 HIS 0.003 0.001 HIS D 593 PHE 0.017 0.002 PHE B 735 TYR 0.022 0.002 TYR D 478 ARG 0.007 0.001 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.7538 (mtpp) cc_final: 0.7246 (mtmt) REVERT: A 566 TYR cc_start: 0.7581 (m-10) cc_final: 0.7156 (m-10) REVERT: A 591 ASN cc_start: 0.7994 (t0) cc_final: 0.7749 (t0) REVERT: A 715 SER cc_start: 0.7365 (OUTLIER) cc_final: 0.6849 (p) REVERT: A 719 LYS cc_start: 0.8044 (pptt) cc_final: 0.7619 (mtpp) REVERT: A 796 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7288 (mt-10) REVERT: B 691 MET cc_start: 0.7354 (ttp) cc_final: 0.7091 (ttt) REVERT: B 790 LYS cc_start: 0.7606 (mptp) cc_final: 0.7180 (mmmt) REVERT: B 825 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 434 ILE cc_start: 0.8599 (mp) cc_final: 0.8319 (mm) REVERT: C 468 ARG cc_start: 0.7016 (ttm110) cc_final: 0.6724 (mtm110) REVERT: C 487 LYS cc_start: 0.7433 (mtpp) cc_final: 0.7057 (mtmt) REVERT: C 584 PHE cc_start: 0.6415 (t80) cc_final: 0.6170 (t80) REVERT: C 591 ASN cc_start: 0.8124 (t0) cc_final: 0.7908 (t0) REVERT: C 696 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7196 (mtmt) REVERT: C 719 LYS cc_start: 0.8431 (pptt) cc_final: 0.7851 (mtpp) REVERT: C 796 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6961 (mt-10) REVERT: C 800 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6826 (ttm-80) REVERT: C 845 LYS cc_start: 0.6916 (tptt) cc_final: 0.6656 (tppt) REVERT: D 790 LYS cc_start: 0.7479 (mptp) cc_final: 0.6929 (mmmt) REVERT: D 819 ASN cc_start: 0.8132 (m110) cc_final: 0.7904 (m-40) REVERT: D 825 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7997 (mt) outliers start: 31 outliers final: 17 residues processed: 215 average time/residue: 0.2873 time to fit residues: 89.1928 Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN A 747 GLN B 456 ASN B 495 ASN D 456 ASN D 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14708 Z= 0.263 Angle : 0.705 11.070 19782 Z= 0.346 Chirality : 0.046 0.176 2158 Planarity : 0.005 0.043 2390 Dihedral : 20.928 140.460 2894 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.54 % Favored : 91.99 % Rotamer: Outliers : 2.83 % Allowed : 11.95 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.19), residues: 1672 helix: -0.85 (0.17), residues: 852 sheet: -2.79 (0.34), residues: 154 loop : -2.93 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 798 HIS 0.003 0.001 HIS B 593 PHE 0.019 0.002 PHE D 584 TYR 0.021 0.002 TYR D 844 ARG 0.008 0.001 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.622 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: 0.7203 (t0) REVERT: A 487 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7289 (mtmt) REVERT: A 566 TYR cc_start: 0.7633 (m-10) cc_final: 0.7118 (m-10) REVERT: A 664 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: A 703 ASP cc_start: 0.7607 (t70) cc_final: 0.7069 (t0) REVERT: A 715 SER cc_start: 0.7216 (OUTLIER) cc_final: 0.6711 (p) REVERT: A 719 LYS cc_start: 0.8081 (pptt) cc_final: 0.7789 (mtpp) REVERT: A 796 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7178 (mt-10) REVERT: B 669 ASP cc_start: 0.7549 (t70) cc_final: 0.7118 (t70) REVERT: B 677 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.5779 (mp10) REVERT: B 691 MET cc_start: 0.7370 (ttp) cc_final: 0.7127 (ttt) REVERT: B 790 LYS cc_start: 0.7615 (mptp) cc_final: 0.7276 (tptt) REVERT: B 825 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7917 (mt) REVERT: C 434 ILE cc_start: 0.8578 (mp) cc_final: 0.8296 (mm) REVERT: C 487 LYS cc_start: 0.7434 (mtpp) cc_final: 0.7118 (mtmt) REVERT: C 584 PHE cc_start: 0.6357 (t80) cc_final: 0.6110 (t80) REVERT: C 591 ASN cc_start: 0.8220 (t0) cc_final: 0.7998 (t0) REVERT: C 696 LYS cc_start: 0.7606 (mtpt) cc_final: 0.7147 (mtmt) REVERT: C 719 LYS cc_start: 0.8483 (pptt) cc_final: 0.7898 (mtpp) REVERT: C 796 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7104 (mt-10) REVERT: C 800 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.6913 (ttm-80) REVERT: D 743 GLU cc_start: 0.8146 (mp0) cc_final: 0.7694 (mp0) REVERT: D 790 LYS cc_start: 0.7451 (mptp) cc_final: 0.7127 (tptt) REVERT: D 819 ASN cc_start: 0.8216 (m110) cc_final: 0.7984 (m110) REVERT: D 825 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7971 (mt) outliers start: 41 outliers final: 23 residues processed: 186 average time/residue: 0.2846 time to fit residues: 78.0064 Evaluate side-chains 171 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 151 optimal weight: 0.8980 chunk 114 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14708 Z= 0.203 Angle : 0.651 10.088 19782 Z= 0.319 Chirality : 0.044 0.187 2158 Planarity : 0.004 0.043 2390 Dihedral : 20.064 140.493 2894 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 3.25 % Allowed : 12.36 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1672 helix: -0.14 (0.18), residues: 864 sheet: -2.69 (0.34), residues: 160 loop : -2.89 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 798 HIS 0.002 0.000 HIS B 593 PHE 0.015 0.001 PHE D 584 TYR 0.020 0.001 TYR D 844 ARG 0.010 0.001 ARG B 712 *********************** 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 197 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 1.537 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: 0.7710 (t70) cc_final: 0.7234 (t0) REVERT: A 487 LYS cc_start: 0.7514 (mtpp) cc_final: 0.7185 (mtpt) REVERT: A 566 TYR cc_start: 0.7633 (m-10) cc_final: 0.7114 (m-10) REVERT: A 639 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8215 (tp) REVERT: A 664 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7842 (mtt) REVERT: A 703 ASP cc_start: 0.7713 (t70) cc_final: 0.7201 (t0) REVERT: A 715 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6714 (p) REVERT: A 719 LYS cc_start: 0.8044 (pptt) cc_final: 0.7681 (mtpp) REVERT: B 669 ASP cc_start: 0.7551 (t70) cc_final: 0.7119 (t70) REVERT: B 691 MET cc_start: 0.7355 (ttp) cc_final: 0.7125 (ttt) REVERT: B 743 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: B 825 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7910 (mt) REVERT: C 434 ILE cc_start: 0.8597 (mp) cc_final: 0.8327 (mm) REVERT: C 487 LYS cc_start: 0.7365 (mtpp) cc_final: 0.7020 (mtmt) REVERT: C 584 PHE cc_start: 0.6314 (t80) cc_final: 0.6053 (t80) REVERT: C 591 ASN cc_start: 0.8196 (t0) cc_final: 0.7970 (t0) REVERT: C 696 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7188 (mtmt) REVERT: C 719 LYS cc_start: 0.8464 (pptt) cc_final: 0.7898 (mtpp) REVERT: C 733 TYR cc_start: 0.7537 (t80) cc_final: 0.7306 (t80) REVERT: C 796 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7139 (mt-10) REVERT: C 800 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.6846 (ttm-80) REVERT: D 677 GLN cc_start: 0.6735 (mp10) cc_final: 0.6401 (mp10) REVERT: D 743 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: D 790 LYS cc_start: 0.7418 (mptp) cc_final: 0.7212 (tptt) REVERT: D 793 MET cc_start: 0.7468 (mmt) cc_final: 0.6931 (mtt) REVERT: D 819 ASN cc_start: 0.8161 (m110) cc_final: 0.7954 (m110) REVERT: D 825 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7953 (mt) outliers start: 47 outliers final: 26 residues processed: 183 average time/residue: 0.2913 time to fit residues: 77.6510 Evaluate side-chains 173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 639 ILE 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 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 737 MET Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 754 GLN D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14708 Z= 0.261 Angle : 0.672 9.474 19782 Z= 0.327 Chirality : 0.045 0.193 2158 Planarity : 0.004 0.052 2390 Dihedral : 19.540 140.455 2894 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.78 % Favored : 91.87 % Rotamer: Outliers : 3.52 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1672 helix: 0.16 (0.18), residues: 864 sheet: -2.61 (0.34), residues: 160 loop : -2.80 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 706 HIS 0.002 0.001 HIS A 593 PHE 0.015 0.002 PHE D 584 TYR 0.021 0.002 TYR D 844 ARG 0.007 0.001 ARG D 712 *********************** 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 201 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7736 (t70) cc_final: 0.7237 (t0) REVERT: A 487 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7208 (mtmt) REVERT: A 566 TYR cc_start: 0.7645 (m-10) cc_final: 0.7120 (m-10) REVERT: A 703 ASP cc_start: 0.7675 (t70) cc_final: 0.7145 (t0) REVERT: A 715 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6691 (p) REVERT: A 719 LYS cc_start: 0.8027 (pptt) cc_final: 0.7735 (mtpp) REVERT: B 669 ASP cc_start: 0.7751 (t70) cc_final: 0.7467 (t70) REVERT: B 677 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.5799 (mp10) REVERT: B 691 MET cc_start: 0.7371 (ttp) cc_final: 0.7152 (ttt) REVERT: B 743 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: B 793 MET cc_start: 0.7903 (tpt) cc_final: 0.7633 (mtt) REVERT: B 825 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7932 (mt) REVERT: C 434 ILE cc_start: 0.8608 (mp) cc_final: 0.8341 (mm) REVERT: C 487 LYS cc_start: 0.7291 (mtpp) cc_final: 0.6976 (mtpt) REVERT: C 584 PHE cc_start: 0.6374 (t80) cc_final: 0.6096 (t80) REVERT: C 591 ASN cc_start: 0.8156 (t0) cc_final: 0.7926 (t0) REVERT: C 696 LYS cc_start: 0.7629 (mtpt) cc_final: 0.7184 (mtmt) REVERT: C 709 MET cc_start: 0.6632 (mtt) cc_final: 0.5927 (mtm) REVERT: C 719 LYS cc_start: 0.8433 (pptt) cc_final: 0.7867 (mtpp) REVERT: C 796 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7137 (mt-10) REVERT: C 800 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.6949 (ttm-80) REVERT: D 677 GLN cc_start: 0.6600 (mp10) cc_final: 0.6246 (mm-40) REVERT: D 743 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: D 790 LYS cc_start: 0.7506 (mptp) cc_final: 0.7274 (tptt) REVERT: D 793 MET cc_start: 0.7582 (mmt) cc_final: 0.6986 (mtt) REVERT: D 819 ASN cc_start: 0.8232 (m110) cc_final: 0.7978 (m110) REVERT: D 825 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7974 (mt) outliers start: 51 outliers final: 31 residues processed: 189 average time/residue: 0.2820 time to fit residues: 78.1573 Evaluate side-chains 179 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14708 Z= 0.248 Angle : 0.657 9.598 19782 Z= 0.320 Chirality : 0.044 0.181 2158 Planarity : 0.004 0.042 2390 Dihedral : 19.043 140.440 2894 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.48 % Favored : 92.17 % Rotamer: Outliers : 3.31 % Allowed : 12.64 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1672 helix: 0.42 (0.18), residues: 864 sheet: -2.32 (0.37), residues: 132 loop : -2.76 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 706 HIS 0.002 0.001 HIS A 593 PHE 0.013 0.002 PHE D 584 TYR 0.022 0.002 TYR B 844 ARG 0.006 0.001 ARG D 712 *********************** 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 195 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7742 (t70) cc_final: 0.7230 (t0) REVERT: A 487 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7144 (mtmt) REVERT: A 566 TYR cc_start: 0.7649 (m-10) cc_final: 0.7120 (m-10) REVERT: A 703 ASP cc_start: 0.7661 (t70) cc_final: 0.7157 (t0) REVERT: A 706 TRP cc_start: 0.7752 (t-100) cc_final: 0.7519 (t-100) REVERT: A 715 SER cc_start: 0.7232 (OUTLIER) cc_final: 0.6744 (p) REVERT: A 719 LYS cc_start: 0.8066 (pptt) cc_final: 0.7708 (mtpp) REVERT: A 800 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.6813 (ptm160) REVERT: B 677 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.5795 (mp10) REVERT: B 691 MET cc_start: 0.7346 (ttp) cc_final: 0.7133 (ttt) REVERT: B 743 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: B 793 MET cc_start: 0.7757 (tpt) cc_final: 0.7446 (mtt) REVERT: B 825 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7952 (mt) REVERT: C 434 ILE cc_start: 0.8602 (mp) cc_final: 0.8335 (mm) REVERT: C 487 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6972 (mtpt) REVERT: C 584 PHE cc_start: 0.6471 (t80) cc_final: 0.6185 (t80) REVERT: C 591 ASN cc_start: 0.8129 (t0) cc_final: 0.7921 (t0) REVERT: C 696 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7207 (mtmt) REVERT: C 709 MET cc_start: 0.6438 (mtt) cc_final: 0.5739 (mtm) REVERT: C 719 LYS cc_start: 0.8476 (pptt) cc_final: 0.7869 (mtpp) REVERT: C 796 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7148 (mt-10) REVERT: C 800 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.6834 (ttm-80) REVERT: D 677 GLN cc_start: 0.6602 (mp10) cc_final: 0.6274 (mm-40) REVERT: D 743 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: D 819 ASN cc_start: 0.8232 (m110) cc_final: 0.7993 (m110) REVERT: D 825 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7973 (mt) outliers start: 48 outliers final: 34 residues processed: 181 average time/residue: 0.2692 time to fit residues: 71.4316 Evaluate side-chains 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 91 optimal weight: 0.3980 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14708 Z= 0.198 Angle : 0.640 9.120 19782 Z= 0.313 Chirality : 0.043 0.181 2158 Planarity : 0.004 0.046 2390 Dihedral : 18.618 140.490 2894 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.42 % Favored : 92.22 % Rotamer: Outliers : 2.76 % Allowed : 14.09 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1672 helix: 0.70 (0.18), residues: 864 sheet: -2.24 (0.38), residues: 130 loop : -2.66 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 706 HIS 0.001 0.000 HIS B 593 PHE 0.011 0.001 PHE D 584 TYR 0.021 0.001 TYR D 844 ARG 0.009 0.000 ARG A 748 *********************** 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 188 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7632 (t70) cc_final: 0.7199 (t0) REVERT: A 487 LYS cc_start: 0.7427 (mtpp) cc_final: 0.7108 (mtmt) REVERT: A 566 TYR cc_start: 0.7695 (m-10) cc_final: 0.7186 (m-10) REVERT: A 715 SER cc_start: 0.7205 (OUTLIER) cc_final: 0.6728 (p) REVERT: A 719 LYS cc_start: 0.7885 (pptt) cc_final: 0.7274 (mtpp) REVERT: A 800 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.6831 (ptm160) REVERT: B 677 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.5790 (mp10) REVERT: B 691 MET cc_start: 0.7325 (ttp) cc_final: 0.7111 (ttt) REVERT: B 743 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 793 MET cc_start: 0.7703 (tpt) cc_final: 0.7439 (mtt) REVERT: B 825 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7927 (mt) REVERT: C 434 ILE cc_start: 0.8604 (mp) cc_final: 0.8340 (mm) REVERT: C 487 LYS cc_start: 0.7260 (mtpp) cc_final: 0.7019 (mtpt) REVERT: C 584 PHE cc_start: 0.6563 (t80) cc_final: 0.6287 (t80) REVERT: C 691 MET cc_start: 0.6716 (ttp) cc_final: 0.6470 (ttp) REVERT: C 696 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7193 (mtmt) REVERT: C 719 LYS cc_start: 0.8481 (pptt) cc_final: 0.7887 (mtpp) REVERT: C 796 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7049 (mt-10) REVERT: C 800 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.6658 (ttm-80) REVERT: D 677 GLN cc_start: 0.6668 (mp10) cc_final: 0.6313 (mm-40) REVERT: D 743 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: D 793 MET cc_start: 0.7829 (mmm) cc_final: 0.7314 (mtt) REVERT: D 819 ASN cc_start: 0.8252 (m110) cc_final: 0.8010 (m110) REVERT: D 825 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7952 (mt) outliers start: 40 outliers final: 29 residues processed: 175 average time/residue: 0.2819 time to fit residues: 72.7286 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 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 B residue 825 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.0070 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 593 HIS D 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14708 Z= 0.154 Angle : 0.613 9.019 19782 Z= 0.300 Chirality : 0.042 0.177 2158 Planarity : 0.004 0.045 2390 Dihedral : 18.022 140.654 2894 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.00 % Favored : 92.76 % Rotamer: Outliers : 2.28 % Allowed : 14.71 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1672 helix: 1.15 (0.19), residues: 852 sheet: -2.22 (0.38), residues: 130 loop : -2.61 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 798 HIS 0.003 0.001 HIS D 792 PHE 0.010 0.001 PHE B 708 TYR 0.021 0.001 TYR A 542 ARG 0.008 0.000 ARG A 748 *********************** 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 189 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.518 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: 0.7530 (t70) cc_final: 0.7129 (t0) REVERT: A 487 LYS cc_start: 0.7288 (mtpp) cc_final: 0.6935 (mtpt) REVERT: A 719 LYS cc_start: 0.7835 (pptt) cc_final: 0.7416 (mtpp) REVERT: A 800 ARG cc_start: 0.7359 (tpp-160) cc_final: 0.6926 (ptp-110) REVERT: B 677 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.5815 (mp10) REVERT: B 691 MET cc_start: 0.7296 (ttp) cc_final: 0.7094 (ttt) REVERT: B 743 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 793 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7274 (mtt) REVERT: C 434 ILE cc_start: 0.8641 (mp) cc_final: 0.8374 (mm) REVERT: C 487 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7070 (mtpt) REVERT: C 584 PHE cc_start: 0.6547 (t80) cc_final: 0.6278 (t80) REVERT: C 691 MET cc_start: 0.6593 (ttp) cc_final: 0.6379 (ttp) REVERT: C 696 LYS cc_start: 0.7629 (mtpt) cc_final: 0.7161 (mtmt) REVERT: C 719 LYS cc_start: 0.8490 (pptt) cc_final: 0.7900 (mtpp) REVERT: C 796 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7254 (mt-10) REVERT: D 677 GLN cc_start: 0.6718 (mp10) cc_final: 0.6354 (mm-40) REVERT: D 743 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: D 793 MET cc_start: 0.7626 (mmm) cc_final: 0.7293 (mtt) REVERT: D 825 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7861 (mt) outliers start: 33 outliers final: 20 residues processed: 176 average time/residue: 0.2806 time to fit residues: 72.8901 Evaluate side-chains 170 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 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 603 GLU Chi-restraints excluded: chain B residue 648 ILE 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 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 Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.0020 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14708 Z= 0.218 Angle : 0.644 8.902 19782 Z= 0.314 Chirality : 0.043 0.198 2158 Planarity : 0.004 0.045 2390 Dihedral : 17.796 140.618 2894 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.60 % Favored : 92.11 % Rotamer: Outliers : 2.14 % Allowed : 15.06 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1672 helix: 1.14 (0.18), residues: 852 sheet: -2.15 (0.38), residues: 130 loop : -2.61 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 798 HIS 0.004 0.001 HIS C 792 PHE 0.012 0.001 PHE D 584 TYR 0.023 0.001 TYR D 844 ARG 0.009 0.001 ARG A 748 *********************** 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 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.477 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: 0.7473 (t70) cc_final: 0.7073 (t0) REVERT: A 487 LYS cc_start: 0.7366 (mtpp) cc_final: 0.7039 (mtmt) REVERT: A 719 LYS cc_start: 0.8016 (pptt) cc_final: 0.7538 (mtpp) REVERT: A 800 ARG cc_start: 0.7594 (tpp-160) cc_final: 0.6923 (ptp-110) REVERT: B 677 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.5829 (mp10) REVERT: B 691 MET cc_start: 0.7322 (ttp) cc_final: 0.7121 (ttt) REVERT: B 743 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: B 793 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7407 (mtt) REVERT: B 825 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7953 (mt) REVERT: C 434 ILE cc_start: 0.8641 (mp) cc_final: 0.8383 (mm) REVERT: C 487 LYS cc_start: 0.7434 (mtpp) cc_final: 0.7091 (mtpt) REVERT: C 584 PHE cc_start: 0.6568 (t80) cc_final: 0.6296 (t80) REVERT: C 691 MET cc_start: 0.6655 (ttp) cc_final: 0.6425 (ttp) REVERT: C 696 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7183 (mtmt) REVERT: C 719 LYS cc_start: 0.8473 (pptt) cc_final: 0.7873 (mtpp) REVERT: C 796 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6951 (mm-30) REVERT: C 800 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.6989 (ttm-80) REVERT: D 677 GLN cc_start: 0.6720 (mp10) cc_final: 0.6392 (mm-40) REVERT: D 743 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: D 793 MET cc_start: 0.7761 (mmm) cc_final: 0.7254 (mtt) REVERT: D 825 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7958 (mt) outliers start: 31 outliers final: 22 residues processed: 167 average time/residue: 0.2835 time to fit residues: 69.1080 Evaluate side-chains 172 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 793 MET 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 552 VAL Chi-restraints excluded: chain B residue 648 ILE 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 B residue 825 ILE 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 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14708 Z= 0.289 Angle : 0.684 8.800 19782 Z= 0.334 Chirality : 0.045 0.196 2158 Planarity : 0.004 0.043 2390 Dihedral : 17.893 140.374 2894 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.11 % Rotamer: Outliers : 2.14 % Allowed : 15.06 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1672 helix: 0.92 (0.18), residues: 852 sheet: -2.16 (0.39), residues: 130 loop : -2.64 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 798 HIS 0.002 0.001 HIS B 593 PHE 0.014 0.002 PHE B 584 TYR 0.023 0.002 TYR D 844 ARG 0.009 0.001 ARG A 748 ********************** 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: 31 poor density : 145 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7454 (t70) cc_final: 0.7073 (t0) REVERT: A 487 LYS cc_start: 0.7295 (mtpp) cc_final: 0.6882 (mtmt) REVERT: A 719 LYS cc_start: 0.7949 (pptt) cc_final: 0.7537 (mtpp) REVERT: A 800 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.6906 (ptm160) REVERT: B 677 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.5568 (mp10) REVERT: B 691 MET cc_start: 0.7320 (ttp) cc_final: 0.7119 (ttt) REVERT: B 743 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: B 793 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7519 (mtt) REVERT: B 825 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8059 (mt) REVERT: C 434 ILE cc_start: 0.8661 (mp) cc_final: 0.8409 (mm) REVERT: C 487 LYS cc_start: 0.7476 (mtpp) cc_final: 0.7226 (mtpt) REVERT: C 584 PHE cc_start: 0.6573 (t80) cc_final: 0.6311 (t80) REVERT: C 691 MET cc_start: 0.6717 (ttp) cc_final: 0.6514 (ttp) REVERT: C 696 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7166 (mtmt) REVERT: C 709 MET cc_start: 0.6663 (mtm) cc_final: 0.5936 (mtm) REVERT: C 719 LYS cc_start: 0.8472 (pptt) cc_final: 0.7853 (mtpp) REVERT: D 677 GLN cc_start: 0.6755 (mp10) cc_final: 0.6428 (mm-40) REVERT: D 743 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: D 793 MET cc_start: 0.7733 (mmm) cc_final: 0.7313 (mtt) REVERT: D 825 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7987 (mt) outliers start: 31 outliers final: 22 residues processed: 164 average time/residue: 0.2924 time to fit residues: 69.6378 Evaluate side-chains 171 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 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 552 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ILE 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 B residue 825 ILE 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 639 ILE Chi-restraints excluded: chain D residue 743 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 825 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149928 restraints weight = 15840.755| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.85 r_work: 0.3337 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14708 Z= 0.158 Angle : 0.618 9.567 19782 Z= 0.302 Chirality : 0.042 0.189 2158 Planarity : 0.004 0.047 2390 Dihedral : 17.478 140.568 2894 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.76 % Favored : 93.00 % Rotamer: Outliers : 2.14 % Allowed : 15.26 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1672 helix: 1.33 (0.19), residues: 852 sheet: -2.14 (0.39), residues: 128 loop : -2.58 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 798 HIS 0.001 0.000 HIS B 508 PHE 0.009 0.001 PHE B 584 TYR 0.020 0.001 TYR D 844 ARG 0.008 0.000 ARG A 748 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.32 seconds wall clock time: 55 minutes 26.08 seconds (3326.08 seconds total)