Starting phenix.real_space_refine on Mon Jan 20 16:37:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxs_47297/01_2025/9dxs_47297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxs_47297/01_2025/9dxs_47297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxs_47297/01_2025/9dxs_47297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxs_47297/01_2025/9dxs_47297.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxs_47297/01_2025/9dxs_47297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxs_47297/01_2025/9dxs_47297.cif" } resolution = 3.55 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= 0.002 sd= 0.059 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 10002 2.51 5 N 2362 2.21 5 O 2818 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 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15294 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 428} Chain: "B" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "C" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 428} Chain: "D" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} 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: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 336 Unusual residues: {'2J9': 1, 'CLR': 3, 'NAG': 1, 'POV': 4, 'SPM': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 164 Unusual residues: {'2J9': 2, 'CLR': 1, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 278 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 176 Unusual residues: {'2J9': 1, 'CLR': 2, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 10.21, per 1000 atoms: 0.67 Number of scatterers: 15294 At special positions: 0 Unit cell: (134.435, 114.395, 141.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 F 4 9.00 O 2818 8.00 N 2362 7.00 C 10002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS D 595 " distance=2.04 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 546 " " NAG C1006 " - " ASN C 546 " " NAG E 1 " - " ASN A 751 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 751 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.2 seconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 51.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.525A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.872A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.800A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.823A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.582A pdb=" N PHE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 665 removed outlier: 4.169A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.502A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.746A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 removed outlier: 3.811A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.846A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 788 removed outlier: 3.508A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 3.673A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 850 removed outlier: 3.640A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 869 removed outlier: 4.151A pdb=" N VAL A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.917A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.160A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.513A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.860A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 633 through 661 removed outlier: 3.652A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.590A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.522A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.706A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.677A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 4.021A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.678A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 783 " --> pdb=" O THR B 779 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 800 removed outlier: 3.517A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.597A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 846 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.774A pdb=" N MET B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.524A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.872A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.802A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.823A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.581A pdb=" N PHE C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 4.169A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.502A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.746A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 730 removed outlier: 3.812A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 730 " --> pdb=" O GLN C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.846A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 788 removed outlier: 3.508A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.671A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 850 removed outlier: 3.640A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 869 removed outlier: 4.152A pdb=" N VAL C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.917A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.161A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.513A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.861A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 632 No H-bonds generated for 'chain 'D' and resid 630 through 632' Processing helix chain 'D' and resid 633 through 661 removed outlier: 3.651A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.590A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.521A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.706A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.677A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 4.021A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 789 removed outlier: 3.677A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.517A pdb=" N ARG D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.597A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 846 " --> pdb=" O PHE D 842 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 848 " --> pdb=" O TYR D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 3.773A pdb=" N MET D 861 " --> pdb=" O PHE D 857 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.574A pdb=" N GLN A 497 " --> pdb=" O ASP A 492 " (cutoff:3.500A) 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 538 through 540 Processing sheet with id=AA5, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.819A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.151A 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: 3.584A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.324A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB3, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.573A pdb=" N GLN C 497 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AB6, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.818A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 436 through 437 Processing sheet with id=AB8, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB9, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.152A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.585A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.324A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 602 hydrogen bonds defined for protein. 1764 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: 4.54 Time building geometry restraints manager: 5.09 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: 2360 1.31 - 1.44: 4098 1.44 - 1.57: 8964 1.57 - 1.70: 47 1.70 - 1.82: 156 Bond restraints: 15625 Sorted by residual: bond pdb=" OAA 2J9 B1001 " pdb=" SAP 2J9 B1001 " 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 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAB 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" OAA 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.650 -0.198 2.00e-02 2.50e+03 9.75e+01 ... (remaining 15620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.52: 20918 6.52 - 13.03: 148 13.03 - 19.55: 0 19.55 - 26.07: 0 26.07 - 32.58: 8 Bond angle restraints: 21074 Sorted by residual: angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 150.25 -32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 D1002 " pdb=" CAN 2J9 D1002 " pdb=" NAO 2J9 D1002 " ideal model delta sigma weight residual 117.67 150.03 -32.36 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAH 2J9 B1001 " pdb=" CAN 2J9 B1001 " pdb=" NAO 2J9 B1001 " ideal model delta sigma weight residual 117.67 149.98 -32.31 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.64 -31.97 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 118.82 150.19 -31.37 3.00e+00 1.11e-01 1.09e+02 ... (remaining 21069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9600 35.97 - 71.94: 369 71.94 - 107.91: 86 107.91 - 143.88: 19 143.88 - 179.85: 6 Dihedral angle restraints: 10080 sinusoidal: 4928 harmonic: 5152 Sorted by residual: dihedral pdb=" CA GLU B 441 " pdb=" C GLU B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta harmonic sigma weight residual 180.00 -118.46 -61.54 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA GLU D 441 " pdb=" C GLU D 441 " pdb=" N PRO D 442 " pdb=" CA PRO D 442 " ideal model delta harmonic sigma weight residual -180.00 -118.46 -61.54 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA ASN A 819 " pdb=" C ASN A 819 " pdb=" N ILE A 820 " pdb=" CA ILE A 820 " ideal model delta harmonic sigma weight residual -180.00 -126.25 -53.75 0 5.00e+00 4.00e-02 1.16e+02 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 2332 1.059 - 2.119: 0 2.119 - 3.178: 4 3.178 - 4.237: 0 4.237 - 5.296: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" C13 CLR C1005 " pdb=" C12 CLR C1005 " pdb=" C14 CLR C1005 " pdb=" C17 CLR C1005 " both_signs ideal model delta sigma weight residual False -2.93 2.36 -5.30 2.00e-01 2.50e+01 7.01e+02 chirality pdb=" C13 CLR A1005 " pdb=" C12 CLR A1005 " pdb=" C14 CLR A1005 " pdb=" C17 CLR A1005 " both_signs ideal model delta sigma weight residual False -2.93 2.36 -5.29 2.00e-01 2.50e+01 6.99e+02 chirality pdb=" CAN 2J9 B1001 " pdb=" CAG 2J9 B1001 " pdb=" CAH 2J9 B1001 " pdb=" NAO 2J9 B1001 " both_signs ideal model delta sigma weight residual True 2.32 0.00 2.32 2.00e-01 2.50e+01 1.34e+02 ... (remaining 2335 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 441 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO D 442 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 442 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 442 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 441 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO B 442 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 515 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO A 516 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.040 5.00e-02 4.00e+02 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2304 2.75 - 3.29: 13969 3.29 - 3.83: 23421 3.83 - 4.36: 27480 4.36 - 4.90: 46583 Nonbonded interactions: 113757 Sorted by model distance: nonbonded pdb=" O VAL A 716 " pdb=" OH TYR A 733 " model vdw 2.217 3.040 nonbonded pdb=" O VAL C 716 " pdb=" OH TYR C 733 " model vdw 2.217 3.040 nonbonded pdb=" ND1 HIS A 593 " pdb=" O PRO D 594 " model vdw 2.298 3.120 nonbonded pdb=" OH TYR C 590 " pdb=" OD1 ASN C 605 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 590 " pdb=" OD1 ASN A 605 " model vdw 2.321 3.040 ... (remaining 113752 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 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'B' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'C' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'D' and (resid 429 through 874 or resid 1003 or resid 1005)) } 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 group one per residue 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: 3.010 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.280 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.011 0.202 15625 Z= 0.676 Angle : 1.466 32.584 21074 Z= 0.643 Chirality : 0.192 5.296 2338 Planarity : 0.007 0.077 2526 Dihedral : 20.284 179.854 6761 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.04 % Favored : 88.40 % Rotamer: Outliers : 0.39 % Allowed : 6.46 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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: -5.80 (0.13), residues: 1776 helix: -3.91 (0.08), residues: 900 sheet: -3.78 (0.37), residues: 130 loop : -3.62 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 589 HIS 0.002 0.001 HIS A 792 PHE 0.020 0.002 PHE B 446 TYR 0.027 0.003 TYR A 733 ARG 0.005 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 649 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8424 (mtpp) REVERT: A 528 ASP cc_start: 0.7270 (m-30) cc_final: 0.6977 (m-30) REVERT: A 549 ASN cc_start: 0.8976 (t0) cc_final: 0.8732 (t0) REVERT: A 590 TYR cc_start: 0.9078 (p90) cc_final: 0.8852 (p90) REVERT: A 605 ASN cc_start: 0.8346 (m110) cc_final: 0.7561 (m-40) REVERT: A 639 ILE cc_start: 0.9485 (tp) cc_final: 0.9270 (tp) REVERT: A 665 GLU cc_start: 0.8918 (tp30) cc_final: 0.8579 (tm-30) REVERT: A 673 ASP cc_start: 0.9305 (m-30) cc_final: 0.9069 (m-30) REVERT: A 685 VAL cc_start: 0.9262 (t) cc_final: 0.8768 (p) REVERT: A 696 LYS cc_start: 0.9621 (mttt) cc_final: 0.9405 (mmtp) REVERT: A 702 TYR cc_start: 0.9571 (m-10) cc_final: 0.9184 (m-80) REVERT: A 704 LYS cc_start: 0.9457 (ptmt) cc_final: 0.9205 (ptmm) REVERT: A 705 MET cc_start: 0.9539 (mtp) cc_final: 0.8935 (mtp) REVERT: A 708 PHE cc_start: 0.9500 (t80) cc_final: 0.8914 (t80) REVERT: A 713 ARG cc_start: 0.8960 (ttt90) cc_final: 0.8732 (mtp-110) REVERT: A 732 ASP cc_start: 0.8650 (m-30) cc_final: 0.8168 (p0) REVERT: A 775 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7770 (ttp-170) REVERT: A 779 THR cc_start: 0.8600 (m) cc_final: 0.8379 (m) REVERT: A 792 HIS cc_start: 0.8931 (t70) cc_final: 0.8698 (t70) REVERT: A 818 GLN cc_start: 0.9160 (mp10) cc_final: 0.8926 (mp10) REVERT: A 864 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 441 GLU cc_start: 0.8884 (tp30) cc_final: 0.8566 (tp30) REVERT: B 481 ARG cc_start: 0.7369 (ttm170) cc_final: 0.6953 (mtm-85) REVERT: B 484 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 524 GLU cc_start: 0.8962 (tp30) cc_final: 0.8641 (tp30) REVERT: B 575 SER cc_start: 0.9096 (m) cc_final: 0.8682 (t) REVERT: B 588 GLU cc_start: 0.9541 (tp30) cc_final: 0.9200 (tp30) REVERT: B 589 TRP cc_start: 0.9000 (m100) cc_final: 0.8671 (m-10) REVERT: B 603 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 611 SER cc_start: 0.9246 (m) cc_final: 0.8735 (m) REVERT: B 612 PHE cc_start: 0.8374 (m-80) cc_final: 0.8152 (m-80) REVERT: B 626 LEU cc_start: 0.9268 (pp) cc_final: 0.9042 (pp) REVERT: B 686 GLU cc_start: 0.8810 (tt0) cc_final: 0.8525 (tm-30) REVERT: B 722 GLU cc_start: 0.9137 (tp30) cc_final: 0.8641 (tp30) REVERT: B 779 THR cc_start: 0.9339 (m) cc_final: 0.9017 (p) REVERT: B 784 GLN cc_start: 0.9239 (tt0) cc_final: 0.8735 (tm-30) REVERT: B 787 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9230 (mm-30) REVERT: B 788 GLU cc_start: 0.8939 (mp0) cc_final: 0.8649 (mp0) REVERT: B 795 LYS cc_start: 0.9511 (tttt) cc_final: 0.9221 (tptm) REVERT: B 796 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8942 (mm-30) REVERT: B 797 LYS cc_start: 0.9724 (tttt) cc_final: 0.9295 (tttt) REVERT: B 798 TRP cc_start: 0.9218 (m100) cc_final: 0.8428 (m100) REVERT: B 847 LYS cc_start: 0.7840 (tttt) cc_final: 0.7573 (tppt) REVERT: C 465 ASP cc_start: 0.8382 (m-30) cc_final: 0.8141 (m-30) REVERT: C 478 TYR cc_start: 0.7643 (p90) cc_final: 0.7411 (p90) REVERT: C 487 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8375 (mtpp) REVERT: C 528 ASP cc_start: 0.7312 (m-30) cc_final: 0.6893 (m-30) REVERT: C 603 GLU cc_start: 0.7326 (tp30) cc_final: 0.6999 (tp30) REVERT: C 604 ASN cc_start: 0.8101 (p0) cc_final: 0.7898 (p0) REVERT: C 607 THR cc_start: 0.9339 (p) cc_final: 0.9075 (t) REVERT: C 673 ASP cc_start: 0.9402 (m-30) cc_final: 0.9198 (m-30) REVERT: C 692 THR cc_start: 0.9380 (m) cc_final: 0.9149 (p) REVERT: C 708 PHE cc_start: 0.9282 (t80) cc_final: 0.8987 (t80) REVERT: C 732 ASP cc_start: 0.8534 (m-30) cc_final: 0.8227 (t70) REVERT: C 779 THR cc_start: 0.8520 (m) cc_final: 0.8269 (m) REVERT: C 793 MET cc_start: 0.8764 (mmm) cc_final: 0.8547 (mmm) REVERT: C 842 PHE cc_start: 0.8950 (t80) cc_final: 0.8724 (t80) REVERT: D 479 GLU cc_start: 0.7440 (tt0) cc_final: 0.7139 (tm-30) REVERT: D 484 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 524 GLU cc_start: 0.8922 (tp30) cc_final: 0.8652 (tp30) REVERT: D 575 SER cc_start: 0.9175 (m) cc_final: 0.8802 (t) REVERT: D 588 GLU cc_start: 0.9436 (tp30) cc_final: 0.8871 (tp30) REVERT: D 603 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8050 (mm-30) REVERT: D 625 GLU cc_start: 0.8371 (pm20) cc_final: 0.8073 (pm20) REVERT: D 673 ASP cc_start: 0.9318 (m-30) cc_final: 0.9088 (m-30) REVERT: D 686 GLU cc_start: 0.8792 (tt0) cc_final: 0.8460 (tm-30) REVERT: D 722 GLU cc_start: 0.9149 (tp30) cc_final: 0.8646 (tp30) REVERT: D 784 GLN cc_start: 0.9266 (tt0) cc_final: 0.9038 (tt0) REVERT: D 787 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9263 (mm-30) REVERT: D 795 LYS cc_start: 0.9528 (tttt) cc_final: 0.9296 (tptm) REVERT: D 797 LYS cc_start: 0.9649 (tttt) cc_final: 0.9415 (ttpp) REVERT: D 798 TRP cc_start: 0.9346 (m100) cc_final: 0.8845 (m100) outliers start: 6 outliers final: 0 residues processed: 650 average time/residue: 0.3064 time to fit residues: 282.0622 Evaluate side-chains 409 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0270 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 GLN A 749 ASN B 495 ASN B 549 ASN B 596 ASN C 491 GLN C 605 ASN C 714 GLN C 749 ASN D 495 ASN D 549 ASN D 596 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111124 restraints weight = 26338.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115173 restraints weight = 11837.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117739 restraints weight = 7726.716| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15625 Z= 0.226 Angle : 0.951 31.819 21074 Z= 0.430 Chirality : 0.068 1.741 2338 Planarity : 0.006 0.078 2526 Dihedral : 21.558 170.230 3373 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.42 % Favored : 89.36 % Rotamer: Outliers : 4.13 % Allowed : 14.08 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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: -3.28 (0.17), residues: 1776 helix: -1.12 (0.15), residues: 932 sheet: -2.73 (0.50), residues: 100 loop : -3.51 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 589 HIS 0.003 0.001 HIS A 593 PHE 0.027 0.002 PHE B 529 TYR 0.028 0.002 TYR B 590 ARG 0.007 0.001 ARG A 727 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 453 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 SER cc_start: 0.8844 (t) cc_final: 0.8535 (p) REVERT: A 487 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8776 (mtmm) REVERT: A 549 ASN cc_start: 0.8989 (t0) cc_final: 0.8768 (t0) REVERT: A 605 ASN cc_start: 0.8424 (m110) cc_final: 0.8186 (p0) REVERT: A 665 GLU cc_start: 0.8856 (tp30) cc_final: 0.8616 (tm-30) REVERT: A 673 ASP cc_start: 0.9181 (m-30) cc_final: 0.8734 (m-30) REVERT: A 705 MET cc_start: 0.9499 (mtp) cc_final: 0.9027 (mtp) REVERT: A 713 ARG cc_start: 0.8960 (ttt90) cc_final: 0.8719 (mtp-110) REVERT: A 775 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7954 (ttp-170) REVERT: A 795 LYS cc_start: 0.8941 (tttt) cc_final: 0.8680 (tttp) REVERT: A 819 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8219 (p0) REVERT: B 473 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8751 (mp) REVERT: B 528 ASP cc_start: 0.7743 (m-30) cc_final: 0.7512 (m-30) REVERT: B 566 TYR cc_start: 0.9079 (m-10) cc_final: 0.8752 (m-80) REVERT: B 603 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 611 SER cc_start: 0.9373 (m) cc_final: 0.8941 (m) REVERT: B 632 SER cc_start: 0.9549 (p) cc_final: 0.9321 (t) REVERT: B 784 GLN cc_start: 0.9101 (tt0) cc_final: 0.8718 (tm-30) REVERT: B 788 GLU cc_start: 0.8683 (mp0) cc_final: 0.8317 (mp0) REVERT: B 795 LYS cc_start: 0.9464 (tttt) cc_final: 0.9138 (tptm) REVERT: B 797 LYS cc_start: 0.9704 (tttt) cc_final: 0.9428 (tttt) REVERT: B 798 TRP cc_start: 0.8976 (m100) cc_final: 0.8464 (m100) REVERT: B 844 TYR cc_start: 0.8992 (t80) cc_final: 0.8724 (t80) REVERT: B 861 MET cc_start: 0.8127 (tpt) cc_final: 0.7883 (tpp) REVERT: C 440 GLU cc_start: 0.8282 (tp30) cc_final: 0.8042 (tp30) REVERT: C 487 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8597 (mtmm) REVERT: C 565 MET cc_start: 0.7856 (tpt) cc_final: 0.7648 (mmt) REVERT: C 665 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8309 (mm-30) REVERT: C 673 ASP cc_start: 0.9317 (m-30) cc_final: 0.8808 (m-30) REVERT: C 709 MET cc_start: 0.9338 (mtp) cc_final: 0.9119 (mtp) REVERT: C 748 ARG cc_start: 0.8313 (mmt90) cc_final: 0.7894 (mpt180) REVERT: D 465 ASP cc_start: 0.8866 (t0) cc_final: 0.8543 (t0) REVERT: D 575 SER cc_start: 0.9198 (m) cc_final: 0.8856 (t) REVERT: D 588 GLU cc_start: 0.9431 (tp30) cc_final: 0.9225 (tp30) REVERT: D 603 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8065 (mm-30) REVERT: D 662 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6908 (tm-30) REVERT: D 664 MET cc_start: 0.8310 (pmm) cc_final: 0.7948 (pmm) REVERT: D 797 LYS cc_start: 0.9670 (tttt) cc_final: 0.9297 (tttm) REVERT: D 798 TRP cc_start: 0.9197 (m100) cc_final: 0.8732 (m100) outliers start: 64 outliers final: 34 residues processed: 478 average time/residue: 0.2688 time to fit residues: 191.1508 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 375 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 90 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN B 549 ASN B 621 GLN C 593 HIS C 605 ASN C 677 GLN D 456 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104194 restraints weight = 25918.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108086 restraints weight = 11909.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110577 restraints weight = 7841.520| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15625 Z= 0.235 Angle : 0.913 31.764 21074 Z= 0.406 Chirality : 0.067 1.713 2338 Planarity : 0.005 0.077 2526 Dihedral : 20.192 172.582 3373 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.19 % Favored : 89.53 % Rotamer: Outliers : 4.39 % Allowed : 18.22 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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: -2.18 (0.19), residues: 1776 helix: -0.02 (0.17), residues: 932 sheet: -2.65 (0.50), residues: 88 loop : -3.23 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 589 HIS 0.002 0.001 HIS A 593 PHE 0.020 0.001 PHE A 708 TYR 0.028 0.002 TYR A 733 ARG 0.004 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 399 time to evaluate : 1.684 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 471 SER cc_start: 0.8863 (t) cc_final: 0.8588 (p) REVERT: A 487 LYS cc_start: 0.9152 (mtpp) cc_final: 0.8845 (mtmm) REVERT: A 549 ASN cc_start: 0.8921 (t0) cc_final: 0.8710 (t0) REVERT: A 605 ASN cc_start: 0.8385 (m110) cc_final: 0.8140 (p0) REVERT: A 665 GLU cc_start: 0.8877 (tp30) cc_final: 0.8627 (tm-30) REVERT: A 672 ASP cc_start: 0.8782 (p0) cc_final: 0.8513 (p0) REVERT: A 673 ASP cc_start: 0.9012 (m-30) cc_final: 0.8797 (m-30) REVERT: B 473 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8662 (mp) REVERT: B 504 GLU cc_start: 0.7229 (mp0) cc_final: 0.7002 (mp0) REVERT: B 528 ASP cc_start: 0.7774 (m-30) cc_final: 0.7519 (m-30) REVERT: B 566 TYR cc_start: 0.9078 (m-10) cc_final: 0.8632 (m-80) REVERT: B 603 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7904 (mm-30) REVERT: B 611 SER cc_start: 0.9349 (m) cc_final: 0.9096 (m) REVERT: B 726 GLN cc_start: 0.8960 (mm110) cc_final: 0.8720 (mm-40) REVERT: B 795 LYS cc_start: 0.9472 (tttt) cc_final: 0.9175 (tptm) REVERT: B 797 LYS cc_start: 0.9721 (tttt) cc_final: 0.9421 (tttt) REVERT: B 798 TRP cc_start: 0.9016 (m100) cc_final: 0.8533 (m100) REVERT: B 844 TYR cc_start: 0.8930 (t80) cc_final: 0.8593 (t80) REVERT: B 861 MET cc_start: 0.8118 (tpt) cc_final: 0.7881 (tpp) REVERT: C 440 GLU cc_start: 0.8278 (tp30) cc_final: 0.7911 (tp30) REVERT: C 457 ASP cc_start: 0.8899 (t0) cc_final: 0.8534 (t0) REVERT: C 471 SER cc_start: 0.8785 (t) cc_final: 0.8419 (p) REVERT: C 487 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8669 (mtmm) REVERT: C 498 TRP cc_start: 0.8871 (m100) cc_final: 0.8259 (m100) REVERT: C 565 MET cc_start: 0.7861 (tpt) cc_final: 0.7575 (mmt) REVERT: C 590 TYR cc_start: 0.8460 (p90) cc_final: 0.8010 (p90) REVERT: C 593 HIS cc_start: 0.8710 (m90) cc_final: 0.8426 (m90) REVERT: C 596 ASN cc_start: 0.8500 (t0) cc_final: 0.8297 (t0) REVERT: C 665 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8371 (tp30) REVERT: C 672 ASP cc_start: 0.9021 (p0) cc_final: 0.8794 (p0) REVERT: C 673 ASP cc_start: 0.9254 (m-30) cc_final: 0.9044 (m-30) REVERT: C 709 MET cc_start: 0.9351 (mtp) cc_final: 0.9127 (mtp) REVERT: C 722 GLU cc_start: 0.8336 (tp30) cc_final: 0.8134 (tp30) REVERT: C 754 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8435 (tm-30) REVERT: C 770 MET cc_start: 0.8916 (tpp) cc_final: 0.8471 (tpp) REVERT: C 864 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 504 GLU cc_start: 0.7271 (mp0) cc_final: 0.7049 (mp0) REVERT: D 575 SER cc_start: 0.9199 (m) cc_final: 0.8861 (t) REVERT: D 588 GLU cc_start: 0.9420 (tp30) cc_final: 0.9145 (tp30) REVERT: D 603 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 662 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6426 (tm-30) REVERT: D 793 MET cc_start: 0.9165 (mmt) cc_final: 0.8908 (mmm) REVERT: D 797 LYS cc_start: 0.9648 (tttt) cc_final: 0.9407 (ttpp) REVERT: D 798 TRP cc_start: 0.9238 (m100) cc_final: 0.8922 (m100) outliers start: 68 outliers final: 46 residues processed: 431 average time/residue: 0.2574 time to fit residues: 166.9321 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 364 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 34 optimal weight: 0.0050 chunk 61 optimal weight: 0.0570 chunk 77 optimal weight: 4.9990 overall best weight: 1.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN B 604 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102778 restraints weight = 25963.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106625 restraints weight = 11893.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109093 restraints weight = 7862.170| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15625 Z= 0.249 Angle : 0.894 31.998 21074 Z= 0.395 Chirality : 0.066 1.685 2338 Planarity : 0.005 0.076 2526 Dihedral : 19.076 174.306 3373 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.41 % Rotamer: Outliers : 5.36 % Allowed : 18.73 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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: -1.71 (0.20), residues: 1776 helix: 0.43 (0.17), residues: 942 sheet: -2.61 (0.50), residues: 86 loop : -3.12 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 799 HIS 0.006 0.001 HIS C 593 PHE 0.017 0.001 PHE D 476 TYR 0.018 0.002 TYR D 590 ARG 0.004 0.000 ARG C 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 389 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 471 SER cc_start: 0.8839 (t) cc_final: 0.8555 (p) REVERT: A 487 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8883 (mtmm) REVERT: A 665 GLU cc_start: 0.8903 (tp30) cc_final: 0.8626 (tm-30) REVERT: A 672 ASP cc_start: 0.8857 (p0) cc_final: 0.8577 (p0) REVERT: A 705 MET cc_start: 0.9610 (mtp) cc_final: 0.9124 (mtp) REVERT: A 867 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7851 (ttm) REVERT: A 869 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8373 (tt) REVERT: B 465 ASP cc_start: 0.9096 (m-30) cc_final: 0.8706 (m-30) REVERT: B 473 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 504 GLU cc_start: 0.7306 (mp0) cc_final: 0.7089 (mp0) REVERT: B 528 ASP cc_start: 0.7737 (m-30) cc_final: 0.7508 (m-30) REVERT: B 566 TYR cc_start: 0.9097 (m-10) cc_final: 0.8661 (m-80) REVERT: B 611 SER cc_start: 0.9372 (m) cc_final: 0.9120 (m) REVERT: B 677 GLN cc_start: 0.8888 (tt0) cc_final: 0.8667 (tm-30) REVERT: B 779 THR cc_start: 0.9462 (m) cc_final: 0.9247 (p) REVERT: B 797 LYS cc_start: 0.9734 (tttt) cc_final: 0.9433 (tttt) REVERT: B 861 MET cc_start: 0.8124 (tpt) cc_final: 0.7899 (tpp) REVERT: C 457 ASP cc_start: 0.8955 (t0) cc_final: 0.8604 (t0) REVERT: C 460 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: C 471 SER cc_start: 0.8800 (t) cc_final: 0.8402 (p) REVERT: C 487 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8857 (mtmm) REVERT: C 590 TYR cc_start: 0.8630 (p90) cc_final: 0.8259 (p90) REVERT: C 593 HIS cc_start: 0.8795 (m90) cc_final: 0.8482 (m90) REVERT: C 596 ASN cc_start: 0.8541 (t0) cc_final: 0.8262 (t0) REVERT: C 603 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 620 MET cc_start: 0.8810 (mtp) cc_final: 0.8557 (mtt) REVERT: C 655 LEU cc_start: 0.9287 (tp) cc_final: 0.9050 (tt) REVERT: C 665 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8389 (tp30) REVERT: C 673 ASP cc_start: 0.9296 (m-30) cc_final: 0.9089 (m-30) REVERT: C 709 MET cc_start: 0.9392 (mtp) cc_final: 0.9149 (mtp) REVERT: C 754 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8785 (tm-30) REVERT: C 770 MET cc_start: 0.8967 (tpp) cc_final: 0.8475 (tpp) REVERT: C 864 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D 504 GLU cc_start: 0.7325 (mp0) cc_final: 0.7109 (mp0) REVERT: D 575 SER cc_start: 0.9231 (m) cc_final: 0.8833 (t) REVERT: D 588 GLU cc_start: 0.9428 (tp30) cc_final: 0.9135 (tp30) REVERT: D 603 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 620 MET cc_start: 0.8859 (mmm) cc_final: 0.8619 (mmm) REVERT: D 677 GLN cc_start: 0.8861 (tt0) cc_final: 0.8641 (tm-30) REVERT: D 793 MET cc_start: 0.9179 (mmt) cc_final: 0.8925 (mmm) REVERT: D 796 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8831 (mm-30) REVERT: D 797 LYS cc_start: 0.9672 (tttt) cc_final: 0.9299 (tttp) REVERT: D 798 TRP cc_start: 0.9275 (m100) cc_final: 0.8898 (m100) outliers start: 83 outliers final: 54 residues processed: 428 average time/residue: 0.2491 time to fit residues: 163.2269 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 352 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 0.0060 chunk 25 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN B 604 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105008 restraints weight = 26014.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108988 restraints weight = 11851.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111476 restraints weight = 7811.014| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15625 Z= 0.192 Angle : 0.883 32.234 21074 Z= 0.386 Chirality : 0.066 1.684 2338 Planarity : 0.005 0.092 2526 Dihedral : 18.240 176.756 3373 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.02 % Favored : 89.86 % Rotamer: Outliers : 5.43 % Allowed : 20.28 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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: -1.29 (0.20), residues: 1776 helix: 0.78 (0.17), residues: 942 sheet: -2.44 (0.50), residues: 86 loop : -2.93 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 589 HIS 0.005 0.001 HIS C 593 PHE 0.014 0.001 PHE D 476 TYR 0.028 0.002 TYR B 590 ARG 0.003 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 392 time to evaluate : 1.726 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 460 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 471 SER cc_start: 0.8837 (t) cc_final: 0.8551 (p) REVERT: A 487 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8900 (mtmm) REVERT: A 528 ASP cc_start: 0.7809 (m-30) cc_final: 0.7376 (m-30) REVERT: A 665 GLU cc_start: 0.8918 (tp30) cc_final: 0.8631 (tm-30) REVERT: A 677 GLN cc_start: 0.9038 (tp40) cc_final: 0.8303 (tm-30) REVERT: A 705 MET cc_start: 0.9607 (mtp) cc_final: 0.9151 (mtp) REVERT: A 770 MET cc_start: 0.9019 (tpp) cc_final: 0.8436 (tpp) REVERT: A 788 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: A 869 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 566 TYR cc_start: 0.9107 (m-10) cc_final: 0.8649 (m-80) REVERT: B 589 TRP cc_start: 0.8703 (m100) cc_final: 0.8385 (m100) REVERT: B 611 SER cc_start: 0.9410 (m) cc_final: 0.9193 (m) REVERT: B 620 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8217 (mmm) REVERT: B 687 ASP cc_start: 0.8254 (m-30) cc_final: 0.7872 (m-30) REVERT: B 797 LYS cc_start: 0.9727 (tttt) cc_final: 0.9467 (tttt) REVERT: C 457 ASP cc_start: 0.8953 (t0) cc_final: 0.8618 (t0) REVERT: C 460 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 471 SER cc_start: 0.8776 (t) cc_final: 0.8365 (p) REVERT: C 487 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8795 (mtmm) REVERT: C 488 TYR cc_start: 0.8810 (m-10) cc_final: 0.8598 (m-10) REVERT: C 498 TRP cc_start: 0.9017 (m100) cc_final: 0.8345 (m100) REVERT: C 501 MET cc_start: 0.8859 (mtm) cc_final: 0.8553 (mtp) REVERT: C 590 TYR cc_start: 0.8643 (p90) cc_final: 0.8307 (p90) REVERT: C 593 HIS cc_start: 0.8746 (m90) cc_final: 0.8403 (m90) REVERT: C 596 ASN cc_start: 0.8564 (t0) cc_final: 0.8256 (t0) REVERT: C 603 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7184 (mm-30) REVERT: C 665 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8383 (tp30) REVERT: C 672 ASP cc_start: 0.9191 (p0) cc_final: 0.8890 (p0) REVERT: C 673 ASP cc_start: 0.9289 (m-30) cc_final: 0.9083 (m-30) REVERT: C 709 MET cc_start: 0.9405 (mtp) cc_final: 0.9155 (mtp) REVERT: C 722 GLU cc_start: 0.8478 (tp30) cc_final: 0.8154 (tp30) REVERT: C 754 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8635 (tm-30) REVERT: C 761 SER cc_start: 0.9477 (t) cc_final: 0.9253 (t) REVERT: D 504 GLU cc_start: 0.7291 (mp0) cc_final: 0.7078 (mp0) REVERT: D 575 SER cc_start: 0.9174 (m) cc_final: 0.8753 (t) REVERT: D 588 GLU cc_start: 0.9385 (tp30) cc_final: 0.9079 (tp30) REVERT: D 603 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 611 SER cc_start: 0.9507 (m) cc_final: 0.9217 (m) REVERT: D 687 ASP cc_start: 0.8009 (m-30) cc_final: 0.7678 (m-30) REVERT: D 793 MET cc_start: 0.9175 (mmt) cc_final: 0.8916 (mmm) REVERT: D 796 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8854 (mm-30) REVERT: D 797 LYS cc_start: 0.9665 (tttt) cc_final: 0.9310 (tttp) REVERT: D 818 GLN cc_start: 0.9114 (pm20) cc_final: 0.8873 (pm20) outliers start: 84 outliers final: 54 residues processed: 434 average time/residue: 0.2441 time to fit residues: 162.0369 Evaluate side-chains 417 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 358 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101335 restraints weight = 25935.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105163 restraints weight = 12272.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107591 restraints weight = 8258.548| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15625 Z= 0.243 Angle : 0.892 32.371 21074 Z= 0.391 Chirality : 0.066 1.665 2338 Planarity : 0.005 0.085 2526 Dihedral : 17.781 176.897 3373 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.02 % Favored : 89.86 % Rotamer: Outliers : 5.75 % Allowed : 20.61 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.02 (0.20), residues: 1776 helix: 1.04 (0.18), residues: 944 sheet: -2.33 (0.51), residues: 86 loop : -2.88 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 589 HIS 0.004 0.001 HIS A 593 PHE 0.016 0.001 PHE B 476 TYR 0.031 0.002 TYR A 590 ARG 0.005 0.000 ARG D 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 366 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 487 LYS cc_start: 0.9252 (mtpp) cc_final: 0.8927 (mtmm) REVERT: A 590 TYR cc_start: 0.8787 (p90) cc_final: 0.8531 (p90) REVERT: A 665 GLU cc_start: 0.8866 (tp30) cc_final: 0.8583 (tm-30) REVERT: A 691 MET cc_start: 0.8288 (ptt) cc_final: 0.8043 (pmm) REVERT: A 770 MET cc_start: 0.8946 (tpp) cc_final: 0.8474 (tpp) REVERT: A 788 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: A 867 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7781 (ttm) REVERT: A 869 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 441 GLU cc_start: 0.8811 (tp30) cc_final: 0.8307 (tp30) REVERT: B 465 ASP cc_start: 0.9097 (m-30) cc_final: 0.8781 (m-30) REVERT: B 528 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7328 (t70) REVERT: B 566 TYR cc_start: 0.9123 (m-10) cc_final: 0.8656 (m-80) REVERT: B 589 TRP cc_start: 0.8888 (m100) cc_final: 0.8512 (m100) REVERT: B 611 SER cc_start: 0.9496 (m) cc_final: 0.9280 (m) REVERT: B 620 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8320 (mmm) REVERT: B 687 ASP cc_start: 0.8408 (m-30) cc_final: 0.7991 (m-30) REVERT: B 793 MET cc_start: 0.9117 (mmt) cc_final: 0.8883 (mmm) REVERT: B 797 LYS cc_start: 0.9692 (tttt) cc_final: 0.9463 (tttt) REVERT: C 457 ASP cc_start: 0.8916 (t0) cc_final: 0.8618 (t0) REVERT: C 460 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: C 471 SER cc_start: 0.8755 (t) cc_final: 0.8354 (p) REVERT: C 487 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8825 (mtmm) REVERT: C 501 MET cc_start: 0.8810 (mtm) cc_final: 0.8586 (mtp) REVERT: C 590 TYR cc_start: 0.8634 (p90) cc_final: 0.8344 (p90) REVERT: C 593 HIS cc_start: 0.8771 (m90) cc_final: 0.8451 (m90) REVERT: C 596 ASN cc_start: 0.8583 (t0) cc_final: 0.8266 (t0) REVERT: C 603 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 665 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8356 (tp30) REVERT: C 709 MET cc_start: 0.9363 (mtp) cc_final: 0.9099 (mtp) REVERT: C 722 GLU cc_start: 0.8401 (tp30) cc_final: 0.8109 (tp30) REVERT: C 723 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8561 (pt0) REVERT: C 754 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 864 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 528 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: D 575 SER cc_start: 0.9183 (m) cc_final: 0.8793 (t) REVERT: D 603 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8052 (mm-30) REVERT: D 611 SER cc_start: 0.9550 (m) cc_final: 0.9310 (m) REVERT: D 793 MET cc_start: 0.9139 (mmt) cc_final: 0.8892 (mmm) REVERT: D 796 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8769 (mm-30) REVERT: D 797 LYS cc_start: 0.9657 (tttt) cc_final: 0.9322 (tttp) REVERT: D 818 GLN cc_start: 0.9052 (pm20) cc_final: 0.8828 (pm20) outliers start: 89 outliers final: 63 residues processed: 408 average time/residue: 0.2425 time to fit residues: 151.7629 Evaluate side-chains 421 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 350 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 134 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN D 605 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101279 restraints weight = 26000.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105152 restraints weight = 12265.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107565 restraints weight = 8238.204| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15625 Z= 0.233 Angle : 0.896 32.309 21074 Z= 0.394 Chirality : 0.065 1.667 2338 Planarity : 0.005 0.100 2526 Dihedral : 17.498 177.562 3373 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.41 % Rotamer: Outliers : 5.36 % Allowed : 22.03 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: -0.92 (0.21), residues: 1776 helix: 1.09 (0.17), residues: 954 sheet: -2.23 (0.51), residues: 86 loop : -2.84 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 589 HIS 0.004 0.001 HIS C 593 PHE 0.012 0.001 PHE B 529 TYR 0.034 0.002 TYR D 590 ARG 0.004 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: A 487 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8922 (mtmm) REVERT: A 665 GLU cc_start: 0.8869 (tp30) cc_final: 0.8585 (tm-30) REVERT: A 770 MET cc_start: 0.8958 (tpp) cc_final: 0.8497 (tpp) REVERT: A 788 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: A 869 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8396 (tt) REVERT: B 441 GLU cc_start: 0.8793 (tp30) cc_final: 0.8431 (tp30) REVERT: B 465 ASP cc_start: 0.9097 (m-30) cc_final: 0.8755 (m-30) REVERT: B 528 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7182 (t0) REVERT: B 589 TRP cc_start: 0.8900 (m100) cc_final: 0.8448 (m100) REVERT: B 620 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8330 (mmm) REVERT: B 793 MET cc_start: 0.9133 (mmt) cc_final: 0.8897 (mmm) REVERT: B 797 LYS cc_start: 0.9696 (tttt) cc_final: 0.9442 (tttt) REVERT: C 457 ASP cc_start: 0.8869 (t0) cc_final: 0.8582 (t0) REVERT: C 460 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: C 471 SER cc_start: 0.8773 (t) cc_final: 0.8371 (p) REVERT: C 487 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8844 (mtmm) REVERT: C 590 TYR cc_start: 0.8672 (p90) cc_final: 0.8412 (p90) REVERT: C 593 HIS cc_start: 0.8781 (m90) cc_final: 0.8455 (m90) REVERT: C 596 ASN cc_start: 0.8601 (t0) cc_final: 0.8291 (t0) REVERT: C 603 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7217 (mm-30) REVERT: C 665 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8347 (tp30) REVERT: C 705 MET cc_start: 0.9628 (mtp) cc_final: 0.9331 (mtp) REVERT: C 709 MET cc_start: 0.9337 (mtp) cc_final: 0.9065 (mtp) REVERT: C 722 GLU cc_start: 0.8437 (tp30) cc_final: 0.8125 (tp30) REVERT: C 723 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8563 (pt0) REVERT: C 754 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8613 (tm-30) REVERT: D 441 GLU cc_start: 0.8481 (tp30) cc_final: 0.7910 (tp30) REVERT: D 528 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7224 (t70) REVERT: D 575 SER cc_start: 0.9198 (m) cc_final: 0.8802 (t) REVERT: D 603 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 611 SER cc_start: 0.9556 (m) cc_final: 0.9330 (m) REVERT: D 620 MET cc_start: 0.8898 (mmm) cc_final: 0.8672 (mtp) REVERT: D 793 MET cc_start: 0.9134 (mmt) cc_final: 0.8891 (mmm) REVERT: D 796 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8771 (mm-30) REVERT: D 797 LYS cc_start: 0.9664 (tttt) cc_final: 0.9354 (tttp) REVERT: D 798 TRP cc_start: 0.9266 (m100) cc_final: 0.8895 (m100) outliers start: 83 outliers final: 59 residues processed: 405 average time/residue: 0.2421 time to fit residues: 150.8782 Evaluate side-chains 412 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 346 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099958 restraints weight = 26001.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103728 restraints weight = 12347.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106109 restraints weight = 8335.276| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15625 Z= 0.279 Angle : 0.917 32.288 21074 Z= 0.406 Chirality : 0.066 1.686 2338 Planarity : 0.005 0.094 2526 Dihedral : 17.218 177.324 3373 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.19 % Favored : 89.70 % Rotamer: Outliers : 5.23 % Allowed : 22.67 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -0.80 (0.21), residues: 1776 helix: 1.20 (0.18), residues: 948 sheet: -2.20 (0.50), residues: 86 loop : -2.78 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 589 HIS 0.004 0.001 HIS C 593 PHE 0.018 0.001 PHE B 446 TYR 0.030 0.002 TYR A 590 ARG 0.004 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 360 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 665 GLU cc_start: 0.8822 (tp30) cc_final: 0.8585 (tm-30) REVERT: A 770 MET cc_start: 0.8902 (tpp) cc_final: 0.8457 (tpp) REVERT: A 869 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8390 (tt) REVERT: B 465 ASP cc_start: 0.9101 (m-30) cc_final: 0.8505 (m-30) REVERT: B 528 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7274 (t0) REVERT: B 589 TRP cc_start: 0.9040 (m100) cc_final: 0.8710 (m100) REVERT: B 620 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8324 (mmm) REVERT: B 691 MET cc_start: 0.8555 (ptm) cc_final: 0.8322 (ptt) REVERT: B 793 MET cc_start: 0.9113 (mmt) cc_final: 0.8885 (mmm) REVERT: B 797 LYS cc_start: 0.9686 (tttt) cc_final: 0.9401 (tttp) REVERT: C 457 ASP cc_start: 0.8822 (t0) cc_final: 0.8553 (t0) REVERT: C 460 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: C 471 SER cc_start: 0.8812 (t) cc_final: 0.8378 (p) REVERT: C 590 TYR cc_start: 0.8729 (p90) cc_final: 0.8508 (p90) REVERT: C 593 HIS cc_start: 0.8839 (m90) cc_final: 0.8511 (m90) REVERT: C 596 ASN cc_start: 0.8638 (t0) cc_final: 0.8355 (t0) REVERT: C 603 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7253 (mm-30) REVERT: C 620 MET cc_start: 0.8806 (mmm) cc_final: 0.8580 (mtt) REVERT: C 665 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8341 (tp30) REVERT: C 681 GLU cc_start: 0.8220 (pm20) cc_final: 0.7854 (pm20) REVERT: C 709 MET cc_start: 0.9340 (mtp) cc_final: 0.9037 (mtp) REVERT: C 722 GLU cc_start: 0.8474 (tp30) cc_final: 0.8164 (tp30) REVERT: C 754 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8722 (tm-30) REVERT: D 441 GLU cc_start: 0.8596 (tp30) cc_final: 0.7974 (tp30) REVERT: D 528 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7218 (t70) REVERT: D 575 SER cc_start: 0.9239 (m) cc_final: 0.8845 (t) REVERT: D 603 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8042 (mm-30) REVERT: D 611 SER cc_start: 0.9547 (m) cc_final: 0.9297 (m) REVERT: D 793 MET cc_start: 0.9127 (mmt) cc_final: 0.8888 (mmm) REVERT: D 797 LYS cc_start: 0.9663 (tttt) cc_final: 0.9356 (tttp) REVERT: D 798 TRP cc_start: 0.9268 (m100) cc_final: 0.8897 (m100) outliers start: 81 outliers final: 65 residues processed: 400 average time/residue: 0.2472 time to fit residues: 151.6201 Evaluate side-chains 417 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 346 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098374 restraints weight = 26024.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102092 restraints weight = 12507.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104429 restraints weight = 8490.476| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15625 Z= 0.314 Angle : 0.932 32.285 21074 Z= 0.415 Chirality : 0.067 1.681 2338 Planarity : 0.005 0.093 2526 Dihedral : 17.000 175.201 3373 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.13 % Rotamer: Outliers : 5.36 % Allowed : 22.87 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -0.75 (0.21), residues: 1776 helix: 1.24 (0.17), residues: 942 sheet: -2.18 (0.50), residues: 88 loop : -2.70 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 589 HIS 0.004 0.001 HIS C 593 PHE 0.016 0.001 PHE D 446 TYR 0.028 0.002 TYR D 590 ARG 0.004 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 362 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7246 (pp20) REVERT: A 665 GLU cc_start: 0.8847 (tp30) cc_final: 0.8582 (tm-30) REVERT: A 681 GLU cc_start: 0.7954 (pm20) cc_final: 0.7744 (pm20) REVERT: A 770 MET cc_start: 0.8934 (tpp) cc_final: 0.8481 (tpp) REVERT: A 788 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: A 869 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 528 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7296 (t0) REVERT: B 620 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8328 (mmm) REVERT: B 687 ASP cc_start: 0.8321 (m-30) cc_final: 0.8014 (m-30) REVERT: B 691 MET cc_start: 0.8623 (ptm) cc_final: 0.8415 (ptt) REVERT: B 793 MET cc_start: 0.9163 (mmt) cc_final: 0.8942 (mmm) REVERT: B 797 LYS cc_start: 0.9698 (tttt) cc_final: 0.9432 (tttp) REVERT: C 457 ASP cc_start: 0.8850 (t0) cc_final: 0.8577 (t0) REVERT: C 460 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: C 471 SER cc_start: 0.8824 (t) cc_final: 0.8393 (p) REVERT: C 593 HIS cc_start: 0.8854 (m90) cc_final: 0.8538 (m90) REVERT: C 603 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7218 (mm-30) REVERT: C 665 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8358 (tp30) REVERT: C 681 GLU cc_start: 0.8227 (pm20) cc_final: 0.7897 (pm20) REVERT: C 705 MET cc_start: 0.9628 (mtp) cc_final: 0.9368 (mtp) REVERT: C 722 GLU cc_start: 0.8491 (tp30) cc_final: 0.8224 (tp30) REVERT: C 723 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8579 (pt0) REVERT: C 754 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8733 (tm-30) REVERT: C 836 PHE cc_start: 0.8589 (m-80) cc_final: 0.8255 (m-10) REVERT: D 441 GLU cc_start: 0.8670 (tp30) cc_final: 0.8020 (tp30) REVERT: D 528 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7274 (t70) REVERT: D 575 SER cc_start: 0.9238 (m) cc_final: 0.8866 (t) REVERT: D 576 CYS cc_start: 0.9145 (m) cc_final: 0.8466 (t) REVERT: D 603 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8075 (mm-30) REVERT: D 611 SER cc_start: 0.9543 (m) cc_final: 0.9304 (m) REVERT: D 793 MET cc_start: 0.9166 (mmt) cc_final: 0.8933 (mmm) REVERT: D 797 LYS cc_start: 0.9671 (tttt) cc_final: 0.9363 (tttp) outliers start: 83 outliers final: 70 residues processed: 399 average time/residue: 0.2500 time to fit residues: 151.3386 Evaluate side-chains 431 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 354 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 114 optimal weight: 0.2980 chunk 81 optimal weight: 0.0570 chunk 89 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN C 621 GLN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103014 restraints weight = 25918.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106747 restraints weight = 12224.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109116 restraints weight = 8236.648| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15625 Z= 0.203 Angle : 0.914 32.378 21074 Z= 0.402 Chirality : 0.067 1.693 2338 Planarity : 0.005 0.091 2526 Dihedral : 16.747 177.006 3373 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.19 % Favored : 89.75 % Rotamer: Outliers : 4.33 % Allowed : 24.22 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -0.63 (0.21), residues: 1776 helix: 1.31 (0.18), residues: 948 sheet: -1.99 (0.52), residues: 86 loop : -2.68 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 589 HIS 0.005 0.001 HIS A 593 PHE 0.014 0.001 PHE B 606 TYR 0.027 0.002 TYR D 590 ARG 0.005 0.000 ARG D 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 374 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 528 ASP cc_start: 0.7782 (m-30) cc_final: 0.7497 (m-30) REVERT: A 665 GLU cc_start: 0.8737 (tp30) cc_final: 0.8508 (tm-30) REVERT: A 681 GLU cc_start: 0.7836 (pm20) cc_final: 0.7567 (pm20) REVERT: A 722 GLU cc_start: 0.8405 (tp30) cc_final: 0.8076 (tp30) REVERT: A 770 MET cc_start: 0.8873 (tpp) cc_final: 0.8431 (tpp) REVERT: A 788 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: B 465 ASP cc_start: 0.9046 (m-30) cc_final: 0.8692 (m-30) REVERT: B 528 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7225 (t0) REVERT: B 620 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8443 (mmm) REVERT: B 687 ASP cc_start: 0.8237 (m-30) cc_final: 0.7931 (m-30) REVERT: B 793 MET cc_start: 0.9055 (mmt) cc_final: 0.8827 (mmm) REVERT: B 797 LYS cc_start: 0.9638 (tttt) cc_final: 0.9390 (tttp) REVERT: C 457 ASP cc_start: 0.8714 (t0) cc_final: 0.8468 (t0) REVERT: C 460 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7476 (pp20) REVERT: C 471 SER cc_start: 0.8732 (t) cc_final: 0.8439 (p) REVERT: C 593 HIS cc_start: 0.8756 (m90) cc_final: 0.8461 (m90) REVERT: C 603 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7192 (mm-30) REVERT: C 665 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8292 (tp30) REVERT: C 681 GLU cc_start: 0.8156 (pm20) cc_final: 0.7859 (pm20) REVERT: C 705 MET cc_start: 0.9568 (mtp) cc_final: 0.9315 (mtp) REVERT: C 722 GLU cc_start: 0.8366 (tp30) cc_final: 0.8098 (tp30) REVERT: C 723 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8550 (pt0) REVERT: C 754 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 836 PHE cc_start: 0.8535 (m-80) cc_final: 0.8193 (m-10) REVERT: C 864 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 441 GLU cc_start: 0.8514 (tp30) cc_final: 0.7904 (tp30) REVERT: D 528 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7236 (t70) REVERT: D 575 SER cc_start: 0.9203 (m) cc_final: 0.8845 (t) REVERT: D 603 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8058 (mm-30) REVERT: D 611 SER cc_start: 0.9599 (m) cc_final: 0.9392 (m) REVERT: D 659 LEU cc_start: 0.9287 (mp) cc_final: 0.9051 (mp) REVERT: D 686 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7432 (tm-30) REVERT: D 793 MET cc_start: 0.9083 (mmt) cc_final: 0.8867 (mmm) REVERT: D 797 LYS cc_start: 0.9621 (tttt) cc_final: 0.9337 (tttp) outliers start: 67 outliers final: 57 residues processed: 403 average time/residue: 0.2527 time to fit residues: 153.4878 Evaluate side-chains 426 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103863 restraints weight = 25650.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107674 restraints weight = 11674.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110112 restraints weight = 7694.426| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15625 Z= 0.228 Angle : 0.935 32.508 21074 Z= 0.415 Chirality : 0.066 1.673 2338 Planarity : 0.005 0.096 2526 Dihedral : 16.619 177.241 3373 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.30 % Favored : 89.64 % Rotamer: Outliers : 4.07 % Allowed : 24.81 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -0.62 (0.21), residues: 1776 helix: 1.35 (0.18), residues: 944 sheet: -1.89 (0.52), residues: 86 loop : -2.71 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 589 HIS 0.004 0.001 HIS A 593 PHE 0.016 0.001 PHE B 744 TYR 0.027 0.002 TYR A 733 ARG 0.006 0.000 ARG D 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5725.07 seconds wall clock time: 104 minutes 11.22 seconds (6251.22 seconds total)