Starting phenix.real_space_refine on Tue Dec 31 10:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxs_47297/12_2024/9dxs_47297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxs_47297/12_2024/9dxs_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_47297/12_2024/9dxs_47297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxs_47297/12_2024/9dxs_47297.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxs_47297/12_2024/9dxs_47297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxs_47297/12_2024/9dxs_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-5532/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: 10.06, per 1000 atoms: 0.66 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: 4.75 Conformation dependent library (CDL) restraints added in 2.0 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: 1.40 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: 4.06 Time building geometry restraints manager: 4.99 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: 2.750 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.180 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- 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 : 1.584 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: 0.3042 time to fit residues: 282.6525 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 : 1.754 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 1.669 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 465 ASP cc_start: 0.8668 (m-30) cc_final: 0.8467 (m-30) REVERT: A 471 SER cc_start: 0.8857 (t) cc_final: 0.8536 (p) REVERT: A 487 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8694 (mtmm) REVERT: A 549 ASN cc_start: 0.8946 (t0) cc_final: 0.8725 (t0) REVERT: A 598 ASP cc_start: 0.8469 (m-30) cc_final: 0.8269 (m-30) REVERT: A 605 ASN cc_start: 0.8491 (m110) cc_final: 0.8165 (p0) REVERT: A 665 GLU cc_start: 0.8894 (tp30) cc_final: 0.8656 (tm-30) REVERT: A 673 ASP cc_start: 0.9229 (m-30) cc_final: 0.8771 (m-30) REVERT: A 705 MET cc_start: 0.9553 (mtp) cc_final: 0.9065 (mtp) REVERT: A 713 ARG cc_start: 0.9030 (ttt90) cc_final: 0.8739 (mtp-110) REVERT: A 775 ARG cc_start: 0.8269 (ptm160) cc_final: 0.7923 (ttp-170) REVERT: A 795 LYS cc_start: 0.8913 (tttt) cc_final: 0.8647 (tttp) REVERT: A 819 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8090 (p0) REVERT: B 473 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 528 ASP cc_start: 0.7706 (m-30) cc_final: 0.7452 (m-30) REVERT: B 566 TYR cc_start: 0.9047 (m-10) cc_final: 0.8827 (m-80) REVERT: B 603 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 611 SER cc_start: 0.9276 (m) cc_final: 0.8836 (m) REVERT: B 632 SER cc_start: 0.9552 (p) cc_final: 0.9266 (t) REVERT: B 686 GLU cc_start: 0.8789 (tt0) cc_final: 0.8498 (tm-30) REVERT: B 784 GLN cc_start: 0.9181 (tt0) cc_final: 0.8749 (tm-30) REVERT: B 788 GLU cc_start: 0.8867 (mp0) cc_final: 0.8351 (mp0) REVERT: B 795 LYS cc_start: 0.9470 (tttt) cc_final: 0.9111 (tptm) REVERT: B 797 LYS cc_start: 0.9714 (tttt) cc_final: 0.9432 (tttt) REVERT: B 798 TRP cc_start: 0.8934 (m100) cc_final: 0.8375 (m100) REVERT: B 844 TYR cc_start: 0.8847 (t80) cc_final: 0.8614 (t80) REVERT: B 861 MET cc_start: 0.8149 (tpt) cc_final: 0.7937 (tpp) REVERT: C 440 GLU cc_start: 0.8189 (tp30) cc_final: 0.7961 (tp30) REVERT: C 487 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8511 (mtmm) REVERT: C 565 MET cc_start: 0.7931 (tpt) cc_final: 0.7727 (mmt) REVERT: C 665 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8324 (mm-30) REVERT: C 673 ASP cc_start: 0.9392 (m-30) cc_final: 0.8851 (m-30) REVERT: C 681 GLU cc_start: 0.7793 (pm20) cc_final: 0.7591 (pm20) REVERT: C 709 MET cc_start: 0.9429 (mtp) cc_final: 0.9211 (mtp) REVERT: C 732 ASP cc_start: 0.8528 (m-30) cc_final: 0.8232 (t0) REVERT: C 748 ARG cc_start: 0.8270 (mmt90) cc_final: 0.7807 (mpt180) REVERT: D 465 ASP cc_start: 0.8932 (t0) cc_final: 0.8634 (t0) REVERT: D 575 SER cc_start: 0.9199 (m) cc_final: 0.8836 (t) REVERT: D 603 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8058 (mm-30) REVERT: D 662 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6976 (tm-30) REVERT: D 664 MET cc_start: 0.8484 (pmm) cc_final: 0.8096 (pmm) REVERT: D 686 GLU cc_start: 0.8760 (tt0) cc_final: 0.8487 (tm-30) REVERT: D 770 MET cc_start: 0.8951 (tpp) cc_final: 0.8682 (tpp) REVERT: D 784 GLN cc_start: 0.9176 (tt0) cc_final: 0.8963 (tm-30) REVERT: D 795 LYS cc_start: 0.9459 (tttt) cc_final: 0.9216 (tptm) REVERT: D 797 LYS cc_start: 0.9694 (tttt) cc_final: 0.9298 (tttm) REVERT: D 798 TRP cc_start: 0.9192 (m100) cc_final: 0.8683 (m100) outliers start: 64 outliers final: 34 residues processed: 478 average time/residue: 0.2591 time to fit residues: 185.2418 Evaluate side-chains 415 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 88 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 604 ASN C 593 HIS C 605 ASN C 677 GLN D 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15625 Z= 0.437 Angle : 0.978 31.968 21074 Z= 0.445 Chirality : 0.069 1.731 2338 Planarity : 0.005 0.078 2526 Dihedral : 20.244 170.501 3373 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.54 % Favored : 88.12 % Rotamer: Outliers : 5.10 % Allowed : 18.09 % Favored : 76.81 % 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: -2.29 (0.19), residues: 1776 helix: -0.02 (0.17), residues: 938 sheet: -2.91 (0.41), residues: 130 loop : -3.40 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 589 HIS 0.003 0.001 HIS C 792 PHE 0.020 0.002 PHE A 708 TYR 0.023 0.002 TYR A 733 ARG 0.004 0.001 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 458 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 379 time to evaluate : 1.766 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 465 ASP cc_start: 0.8699 (m-30) cc_final: 0.8489 (m-30) REVERT: A 487 LYS cc_start: 0.9183 (mtpp) cc_final: 0.8752 (mtmm) REVERT: A 549 ASN cc_start: 0.8938 (t0) cc_final: 0.8710 (t0) REVERT: A 605 ASN cc_start: 0.8448 (m110) cc_final: 0.8122 (p0) REVERT: A 665 GLU cc_start: 0.8935 (tp30) cc_final: 0.8682 (tm-30) REVERT: A 672 ASP cc_start: 0.8901 (p0) cc_final: 0.8696 (p0) REVERT: A 673 ASP cc_start: 0.9134 (m-30) cc_final: 0.8902 (m-30) REVERT: A 705 MET cc_start: 0.9570 (mtp) cc_final: 0.9284 (mtp) REVERT: A 867 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8025 (ttm) REVERT: B 473 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 504 GLU cc_start: 0.7538 (mp0) cc_final: 0.7215 (mp0) REVERT: B 566 TYR cc_start: 0.9074 (m-10) cc_final: 0.8721 (m-80) REVERT: B 603 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8025 (mm-30) REVERT: B 611 SER cc_start: 0.9254 (m) cc_final: 0.9006 (m) REVERT: B 632 SER cc_start: 0.9554 (p) cc_final: 0.9353 (t) REVERT: B 686 GLU cc_start: 0.8822 (tt0) cc_final: 0.8514 (tm-30) REVERT: B 726 GLN cc_start: 0.8942 (mm110) cc_final: 0.8675 (mm-40) REVERT: B 795 LYS cc_start: 0.9529 (tttt) cc_final: 0.9088 (tptm) REVERT: B 797 LYS cc_start: 0.9757 (tttt) cc_final: 0.9405 (tttt) REVERT: B 861 MET cc_start: 0.8131 (tpt) cc_final: 0.7927 (tpp) REVERT: C 440 GLU cc_start: 0.8333 (tp30) cc_final: 0.7963 (tp30) REVERT: C 457 ASP cc_start: 0.9079 (t0) cc_final: 0.8725 (t0) REVERT: C 471 SER cc_start: 0.8817 (t) cc_final: 0.8459 (p) REVERT: C 487 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8796 (mtmm) REVERT: C 590 TYR cc_start: 0.8576 (p90) cc_final: 0.8097 (p90) REVERT: C 593 HIS cc_start: 0.8821 (m90) cc_final: 0.8569 (m90) REVERT: C 602 VAL cc_start: 0.8969 (m) cc_final: 0.8710 (t) REVERT: C 665 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8409 (tp30) REVERT: C 673 ASP cc_start: 0.9353 (m-30) cc_final: 0.9069 (m-30) REVERT: C 679 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7979 (tmtt) REVERT: C 732 ASP cc_start: 0.8470 (m-30) cc_final: 0.8133 (t70) REVERT: C 770 MET cc_start: 0.8973 (tpp) cc_final: 0.8383 (tpp) REVERT: C 864 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7531 (mt-10) REVERT: D 504 GLU cc_start: 0.7615 (mp0) cc_final: 0.7286 (mp0) REVERT: D 565 MET cc_start: 0.8357 (mmt) cc_final: 0.8117 (tpp) REVERT: D 603 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7937 (mm-30) REVERT: D 686 GLU cc_start: 0.8802 (tt0) cc_final: 0.8503 (tm-30) REVERT: D 784 GLN cc_start: 0.9312 (tt0) cc_final: 0.9007 (tm-30) REVERT: D 793 MET cc_start: 0.9238 (mmt) cc_final: 0.8980 (mmm) REVERT: D 795 LYS cc_start: 0.9486 (tttt) cc_final: 0.9223 (tptm) REVERT: D 797 LYS cc_start: 0.9717 (tttt) cc_final: 0.9471 (ttpp) REVERT: D 798 TRP cc_start: 0.9260 (m100) cc_final: 0.8819 (m100) outliers start: 79 outliers final: 57 residues processed: 423 average time/residue: 0.2573 time to fit residues: 165.0981 Evaluate side-chains 408 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 522 VAL 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 611 SER 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 755 ILE 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 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 567 VAL 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 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 718 VAL 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 C residue 819 ASN 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 530 SER Chi-restraints excluded: chain D residue 607 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 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 158 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 621 GLN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15625 Z= 0.219 Angle : 0.892 32.010 21074 Z= 0.393 Chirality : 0.067 1.693 2338 Planarity : 0.005 0.081 2526 Dihedral : 19.142 174.577 3373 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.25 % Favored : 89.64 % Rotamer: Outliers : 4.59 % Allowed : 19.19 % Favored : 76.23 % 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: -1.72 (0.20), residues: 1776 helix: 0.46 (0.17), residues: 944 sheet: -2.81 (0.48), residues: 88 loop : -3.18 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 589 HIS 0.006 0.001 HIS C 593 PHE 0.014 0.001 PHE B 529 TYR 0.027 0.002 TYR B 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 470 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 399 time to evaluate : 1.692 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: A 460 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 465 ASP cc_start: 0.8493 (m-30) cc_final: 0.8261 (m-30) REVERT: A 471 SER cc_start: 0.8830 (t) cc_final: 0.8528 (p) REVERT: A 487 LYS cc_start: 0.9223 (mtpp) cc_final: 0.8801 (mtmm) REVERT: A 665 GLU cc_start: 0.8929 (tp30) cc_final: 0.8661 (tm-30) REVERT: A 672 ASP cc_start: 0.8901 (p0) cc_final: 0.8664 (p0) REVERT: A 705 MET cc_start: 0.9553 (mtp) cc_final: 0.9127 (mtp) REVERT: A 754 GLN cc_start: 0.9186 (tt0) cc_final: 0.8835 (tm-30) REVERT: B 504 GLU cc_start: 0.7535 (mp0) cc_final: 0.7250 (mp0) REVERT: B 528 ASP cc_start: 0.7762 (m-30) cc_final: 0.7444 (m-30) REVERT: B 566 TYR cc_start: 0.9094 (m-10) cc_final: 0.8734 (m-80) REVERT: B 589 TRP cc_start: 0.8735 (m100) cc_final: 0.8479 (m100) REVERT: B 603 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 611 SER cc_start: 0.9278 (m) cc_final: 0.9030 (m) REVERT: B 632 SER cc_start: 0.9545 (p) cc_final: 0.9314 (t) REVERT: B 686 GLU cc_start: 0.8805 (tt0) cc_final: 0.8514 (tm-30) REVERT: B 726 GLN cc_start: 0.8907 (mm110) cc_final: 0.8661 (mm-40) REVERT: B 779 THR cc_start: 0.9358 (m) cc_final: 0.9113 (p) REVERT: B 797 LYS cc_start: 0.9745 (tttt) cc_final: 0.9436 (tttt) REVERT: B 861 MET cc_start: 0.8120 (tpt) cc_final: 0.7920 (tpp) REVERT: C 440 GLU cc_start: 0.8138 (tp30) cc_final: 0.7805 (tp30) REVERT: C 457 ASP cc_start: 0.9035 (t0) cc_final: 0.8654 (t0) REVERT: C 460 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: C 471 SER cc_start: 0.8785 (t) cc_final: 0.8420 (p) REVERT: C 487 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8785 (mtmm) REVERT: C 488 TYR cc_start: 0.8946 (m-10) cc_final: 0.8648 (m-10) REVERT: C 590 TYR cc_start: 0.8704 (p90) cc_final: 0.8275 (p90) REVERT: C 593 HIS cc_start: 0.8734 (m90) cc_final: 0.8430 (m90) REVERT: C 665 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8400 (tp30) REVERT: C 709 MET cc_start: 0.9348 (mtp) cc_final: 0.8602 (mtm) REVERT: C 722 GLU cc_start: 0.8562 (tp30) cc_final: 0.8236 (tp30) REVERT: C 732 ASP cc_start: 0.8394 (m-30) cc_final: 0.8040 (t0) REVERT: C 754 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8783 (tm-30) REVERT: C 770 MET cc_start: 0.9067 (tpp) cc_final: 0.8568 (tpp) REVERT: C 864 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7464 (mt-10) REVERT: D 504 GLU cc_start: 0.7565 (mp0) cc_final: 0.7276 (mp0) REVERT: D 528 ASP cc_start: 0.7753 (m-30) cc_final: 0.7547 (m-30) REVERT: D 603 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 662 GLU cc_start: 0.7674 (tm-30) cc_final: 0.6711 (tm-30) REVERT: D 686 GLU cc_start: 0.8742 (tt0) cc_final: 0.8297 (tm-30) REVERT: D 784 GLN cc_start: 0.9238 (tt0) cc_final: 0.8986 (tm-30) REVERT: D 793 MET cc_start: 0.9217 (mmt) cc_final: 0.8999 (mmm) REVERT: D 795 LYS cc_start: 0.9485 (tttt) cc_final: 0.9225 (tptm) REVERT: D 798 TRP cc_start: 0.9267 (m100) cc_final: 0.8769 (m100) outliers start: 71 outliers final: 48 residues processed: 436 average time/residue: 0.2534 time to fit residues: 169.0854 Evaluate side-chains 410 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 560 SER 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 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 820 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 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 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 718 VAL 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 817 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 0.0040 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 C 621 GLN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4036 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= 0.193 Angle : 0.883 32.231 21074 Z= 0.385 Chirality : 0.066 1.673 2338 Planarity : 0.005 0.098 2526 Dihedral : 18.237 176.631 3373 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.91 % Favored : 89.86 % Rotamer: Outliers : 4.97 % Allowed : 20.22 % Favored : 74.81 % 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: -1.30 (0.20), residues: 1776 helix: 0.85 (0.17), residues: 946 sheet: -2.60 (0.49), residues: 88 loop : -3.07 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 589 HIS 0.005 0.001 HIS C 593 PHE 0.018 0.001 PHE B 476 TYR 0.019 0.002 TYR B 590 ARG 0.003 0.000 ARG C 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 472 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 395 time to evaluate : 1.691 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: 0.8404 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: A 465 ASP cc_start: 0.8420 (m-30) cc_final: 0.8206 (m-30) REVERT: A 487 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8832 (mtmm) REVERT: A 528 ASP cc_start: 0.7703 (m-30) cc_final: 0.7399 (m-30) REVERT: A 665 GLU cc_start: 0.8921 (tp30) cc_final: 0.8649 (tm-30) REVERT: A 677 GLN cc_start: 0.9097 (tp40) cc_final: 0.8286 (tm-30) REVERT: A 705 MET cc_start: 0.9539 (mtp) cc_final: 0.9097 (mtp) REVERT: A 770 MET cc_start: 0.8942 (tpp) cc_final: 0.8397 (tpp) REVERT: A 788 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: A 864 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 867 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8032 (ttm) REVERT: B 603 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8018 (mm-30) REVERT: B 611 SER cc_start: 0.9389 (m) cc_final: 0.9184 (m) REVERT: B 620 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: B 632 SER cc_start: 0.9535 (p) cc_final: 0.9314 (t) REVERT: B 686 GLU cc_start: 0.8744 (tt0) cc_final: 0.8297 (tm-30) REVERT: B 779 THR cc_start: 0.9382 (m) cc_final: 0.9157 (p) REVERT: B 797 LYS cc_start: 0.9743 (tttt) cc_final: 0.9461 (tttt) REVERT: C 440 GLU cc_start: 0.8124 (tp30) cc_final: 0.7778 (tp30) REVERT: C 457 ASP cc_start: 0.9069 (t0) cc_final: 0.8700 (t0) REVERT: C 460 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: C 467 LEU cc_start: 0.8552 (tp) cc_final: 0.8295 (tp) REVERT: C 471 SER cc_start: 0.8785 (t) cc_final: 0.8404 (p) REVERT: C 487 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8776 (mtmm) REVERT: C 590 TYR cc_start: 0.8744 (p90) cc_final: 0.8480 (p90) REVERT: C 593 HIS cc_start: 0.8739 (m90) cc_final: 0.8416 (m90) REVERT: C 665 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8393 (tp30) REVERT: C 754 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8757 (tm-30) REVERT: C 864 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7536 (mt-10) REVERT: D 504 GLU cc_start: 0.7596 (mp0) cc_final: 0.7308 (mp0) REVERT: D 603 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 611 SER cc_start: 0.9347 (m) cc_final: 0.9126 (m) REVERT: D 686 GLU cc_start: 0.8653 (tt0) cc_final: 0.8209 (tm-30) REVERT: D 784 GLN cc_start: 0.9203 (tt0) cc_final: 0.8867 (tm-30) REVERT: D 788 GLU cc_start: 0.8954 (mp0) cc_final: 0.8625 (mp0) REVERT: D 793 MET cc_start: 0.9215 (mmt) cc_final: 0.8945 (mmm) REVERT: D 795 LYS cc_start: 0.9501 (tttt) cc_final: 0.9216 (tptm) REVERT: D 797 LYS cc_start: 0.9697 (tttt) cc_final: 0.9327 (tttp) REVERT: D 798 TRP cc_start: 0.9254 (m100) cc_final: 0.8873 (m100) outliers start: 77 outliers final: 50 residues processed: 434 average time/residue: 0.2492 time to fit residues: 164.9150 Evaluate side-chains 406 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 351 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 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 690 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 867 MET Chi-restraints excluded: chain B residue 483 VAL 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 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 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 604 ASN Chi-restraints excluded: chain C residue 605 ASN 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 C residue 869 LEU Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET 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 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 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15625 Z= 0.416 Angle : 0.950 32.163 21074 Z= 0.426 Chirality : 0.068 1.672 2338 Planarity : 0.005 0.098 2526 Dihedral : 17.908 174.174 3373 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.04 % Favored : 88.85 % Rotamer: Outliers : 5.75 % Allowed : 20.99 % Favored : 73.26 % 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: -1.25 (0.20), residues: 1776 helix: 0.95 (0.17), residues: 946 sheet: -2.94 (0.43), residues: 120 loop : -3.05 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 589 HIS 0.003 0.001 HIS A 593 PHE 0.017 0.002 PHE D 476 TYR 0.017 0.002 TYR D 590 ARG 0.006 0.001 ARG D 775 *********************** 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 447 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 358 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: A 487 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8792 (mtmm) REVERT: A 665 GLU cc_start: 0.8940 (tp30) cc_final: 0.8648 (tm-30) REVERT: A 705 MET cc_start: 0.9585 (mtp) cc_final: 0.9134 (mtp) REVERT: A 754 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8637 (tm-30) REVERT: A 858 CYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 864 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7983 (mt-10) REVERT: A 867 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: B 441 GLU cc_start: 0.8987 (tp30) cc_final: 0.8407 (tp30) REVERT: B 465 ASP cc_start: 0.9203 (m-30) cc_final: 0.8577 (m-30) REVERT: B 528 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: B 611 SER cc_start: 0.9353 (m) cc_final: 0.9123 (m) REVERT: B 632 SER cc_start: 0.9538 (p) cc_final: 0.9307 (t) REVERT: B 686 GLU cc_start: 0.8843 (tt0) cc_final: 0.8501 (tm-30) REVERT: B 779 THR cc_start: 0.9460 (m) cc_final: 0.9222 (p) REVERT: B 793 MET cc_start: 0.9362 (tpp) cc_final: 0.9071 (mmm) REVERT: B 797 LYS cc_start: 0.9745 (tttt) cc_final: 0.9419 (tttt) REVERT: C 440 GLU cc_start: 0.8225 (tp30) cc_final: 0.7885 (tp30) REVERT: C 457 ASP cc_start: 0.9085 (t0) cc_final: 0.8739 (t0) REVERT: C 460 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: C 471 SER cc_start: 0.8855 (t) cc_final: 0.8451 (p) REVERT: C 487 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8772 (mtmm) REVERT: C 501 MET cc_start: 0.8773 (mtm) cc_final: 0.8479 (mtp) REVERT: C 590 TYR cc_start: 0.8802 (p90) cc_final: 0.8528 (p90) REVERT: C 593 HIS cc_start: 0.8850 (m90) cc_final: 0.8527 (m90) REVERT: C 665 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8405 (tp30) REVERT: C 681 GLU cc_start: 0.8241 (pm20) cc_final: 0.7864 (pm20) REVERT: C 691 MET cc_start: 0.9186 (ptp) cc_final: 0.8954 (ptp) REVERT: C 705 MET cc_start: 0.9696 (mtp) cc_final: 0.9424 (mtp) REVERT: C 732 ASP cc_start: 0.8388 (m-30) cc_final: 0.8141 (t0) REVERT: C 754 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8820 (tm-30) REVERT: C 836 PHE cc_start: 0.8535 (m-80) cc_final: 0.8263 (m-10) REVERT: C 864 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 504 GLU cc_start: 0.7628 (mp0) cc_final: 0.7336 (mp0) REVERT: D 528 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7258 (t70) REVERT: D 603 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8034 (mm-30) REVERT: D 611 SER cc_start: 0.9360 (m) cc_final: 0.9146 (m) REVERT: D 686 GLU cc_start: 0.8780 (tt0) cc_final: 0.8478 (tm-30) REVERT: D 784 GLN cc_start: 0.9289 (tt0) cc_final: 0.9012 (tm-30) REVERT: D 793 MET cc_start: 0.9261 (mmt) cc_final: 0.9021 (mmm) REVERT: D 797 LYS cc_start: 0.9730 (tttt) cc_final: 0.9357 (tttp) outliers start: 89 outliers final: 64 residues processed: 403 average time/residue: 0.2480 time to fit residues: 153.3194 Evaluate side-chains 412 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 342 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 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 611 SER Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 858 CYS 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 680 ILE 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 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 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 577 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 611 SER 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 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain D residue 467 LEU 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 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 839 VAL 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 19 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4381 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= 0.202 Angle : 0.902 32.209 21074 Z= 0.395 Chirality : 0.066 1.688 2338 Planarity : 0.005 0.087 2526 Dihedral : 17.496 176.418 3373 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.70 % Favored : 89.25 % Rotamer: Outliers : 4.59 % Allowed : 23.32 % Favored : 72.09 % 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: -0.97 (0.21), residues: 1776 helix: 1.16 (0.18), residues: 944 sheet: -2.39 (0.51), residues: 88 loop : -2.96 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 589 HIS 0.005 0.001 HIS C 593 PHE 0.019 0.001 PHE D 476 TYR 0.037 0.002 TYR D 590 ARG 0.003 0.000 ARG D 712 *********************** 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 455 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 384 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: A 471 SER cc_start: 0.8797 (t) cc_final: 0.8469 (p) REVERT: A 487 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8814 (mtmm) REVERT: A 665 GLU cc_start: 0.8902 (tp30) cc_final: 0.8649 (tm-30) REVERT: A 691 MET cc_start: 0.8252 (ptt) cc_final: 0.8019 (pmm) REVERT: A 705 MET cc_start: 0.9544 (mtp) cc_final: 0.9213 (mtp) REVERT: A 770 MET cc_start: 0.9054 (tpp) cc_final: 0.8514 (tpp) REVERT: A 788 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: A 864 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 867 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: B 441 GLU cc_start: 0.8903 (tp30) cc_final: 0.8476 (tp30) REVERT: B 465 ASP cc_start: 0.9161 (m-30) cc_final: 0.8524 (m-30) REVERT: B 528 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7099 (t0) REVERT: B 603 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 632 SER cc_start: 0.9515 (p) cc_final: 0.9270 (t) REVERT: B 686 GLU cc_start: 0.8652 (tt0) cc_final: 0.8382 (tm-30) REVERT: B 738 GLU cc_start: 0.8750 (mp0) cc_final: 0.8542 (mp0) REVERT: B 779 THR cc_start: 0.9446 (m) cc_final: 0.9220 (p) REVERT: B 793 MET cc_start: 0.9371 (tpp) cc_final: 0.9083 (mmm) REVERT: B 797 LYS cc_start: 0.9727 (tttt) cc_final: 0.9390 (tttp) REVERT: C 457 ASP cc_start: 0.9042 (t0) cc_final: 0.8688 (t0) REVERT: C 460 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: C 471 SER cc_start: 0.8779 (t) cc_final: 0.8493 (p) REVERT: C 487 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8699 (mtmm) REVERT: C 590 TYR cc_start: 0.8824 (p90) cc_final: 0.8569 (p90) REVERT: C 593 HIS cc_start: 0.8790 (m90) cc_final: 0.8454 (m90) REVERT: C 665 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8386 (tp30) REVERT: C 681 GLU cc_start: 0.8272 (pm20) cc_final: 0.7919 (pm20) REVERT: C 709 MET cc_start: 0.9275 (mtp) cc_final: 0.8692 (mtm) REVERT: C 722 GLU cc_start: 0.8417 (tp30) cc_final: 0.8167 (tp30) REVERT: C 723 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8619 (pt0) REVERT: C 754 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8720 (tm-30) REVERT: C 864 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 504 GLU cc_start: 0.7543 (mp0) cc_final: 0.7268 (mp0) REVERT: D 528 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7208 (t70) REVERT: D 603 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8005 (mm-30) REVERT: D 686 GLU cc_start: 0.8642 (tt0) cc_final: 0.8148 (tm-30) REVERT: D 687 ASP cc_start: 0.8629 (m-30) cc_final: 0.7662 (m-30) REVERT: D 784 GLN cc_start: 0.9229 (tt0) cc_final: 0.8900 (tm-30) REVERT: D 788 GLU cc_start: 0.8983 (mp0) cc_final: 0.8679 (mp0) REVERT: D 793 MET cc_start: 0.9240 (mmt) cc_final: 0.8989 (mmm) REVERT: D 797 LYS cc_start: 0.9689 (tttt) cc_final: 0.9401 (tttt) REVERT: D 798 TRP cc_start: 0.9248 (m100) cc_final: 0.8747 (m100) REVERT: D 818 GLN cc_start: 0.9101 (pm20) cc_final: 0.8883 (pm20) outliers start: 71 outliers final: 53 residues processed: 417 average time/residue: 0.2624 time to fit residues: 165.8788 Evaluate side-chains 413 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 354 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 560 SER Chi-restraints excluded: chain A residue 565 MET 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 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE 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 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 565 MET 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 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 LEU 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 737 MET Chi-restraints excluded: chain D residue 752 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15625 Z= 0.344 Angle : 0.942 32.172 21074 Z= 0.420 Chirality : 0.067 1.685 2338 Planarity : 0.005 0.089 2526 Dihedral : 17.314 175.035 3373 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.37 % Favored : 88.51 % Rotamer: Outliers : 4.59 % Allowed : 23.32 % 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: -0.87 (0.21), residues: 1776 helix: 1.25 (0.18), residues: 940 sheet: -2.40 (0.51), residues: 88 loop : -2.91 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 589 HIS 0.003 0.001 HIS C 593 PHE 0.018 0.002 PHE B 446 TYR 0.029 0.002 TYR D 590 ARG 0.005 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 426 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 355 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 487 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8909 (mtmm) REVERT: A 665 GLU cc_start: 0.8912 (tp30) cc_final: 0.8658 (tm-30) REVERT: A 691 MET cc_start: 0.8501 (ptt) cc_final: 0.8177 (ptt) REVERT: A 705 MET cc_start: 0.9573 (mtp) cc_final: 0.9161 (mtp) REVERT: A 770 MET cc_start: 0.9005 (tpp) cc_final: 0.8512 (tpp) REVERT: A 864 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7898 (mt-10) REVERT: B 465 ASP cc_start: 0.9201 (m-30) cc_final: 0.8554 (m-30) REVERT: B 528 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7274 (t70) REVERT: B 603 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 686 GLU cc_start: 0.8752 (tt0) cc_final: 0.8263 (tm-30) REVERT: B 691 MET cc_start: 0.8620 (ptm) cc_final: 0.8336 (ptt) REVERT: B 738 GLU cc_start: 0.8850 (mp0) cc_final: 0.8628 (mp0) REVERT: B 793 MET cc_start: 0.9375 (tpp) cc_final: 0.9100 (mmm) REVERT: B 797 LYS cc_start: 0.9733 (tttt) cc_final: 0.9399 (tttp) REVERT: C 457 ASP cc_start: 0.9084 (t0) cc_final: 0.8756 (t0) REVERT: C 460 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: C 471 SER cc_start: 0.8944 (t) cc_final: 0.8558 (p) REVERT: C 487 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8836 (mtmm) REVERT: C 590 TYR cc_start: 0.8858 (p90) cc_final: 0.8646 (p90) REVERT: C 593 HIS cc_start: 0.8829 (m90) cc_final: 0.8525 (m90) REVERT: C 603 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7015 (mm-30) REVERT: C 681 GLU cc_start: 0.8169 (pm20) cc_final: 0.7929 (pm20) REVERT: C 705 MET cc_start: 0.9696 (mtp) cc_final: 0.9201 (mtp) REVERT: C 709 MET cc_start: 0.9348 (mtp) cc_final: 0.8759 (mtm) REVERT: C 722 GLU cc_start: 0.8504 (tp30) cc_final: 0.8227 (tp30) REVERT: C 723 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8643 (pt0) REVERT: C 754 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8790 (tm-30) REVERT: C 864 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7637 (mt-10) REVERT: D 441 GLU cc_start: 0.8909 (tp30) cc_final: 0.8432 (tp30) REVERT: D 504 GLU cc_start: 0.7628 (mp0) cc_final: 0.7344 (mp0) REVERT: D 528 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7313 (t70) REVERT: D 603 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 686 GLU cc_start: 0.8728 (tt0) cc_final: 0.8163 (tm-30) REVERT: D 687 ASP cc_start: 0.8864 (m-30) cc_final: 0.7574 (m-30) REVERT: D 784 GLN cc_start: 0.9276 (tt0) cc_final: 0.9035 (tm-30) REVERT: D 793 MET cc_start: 0.9271 (mmt) cc_final: 0.9036 (mmm) REVERT: D 797 LYS cc_start: 0.9700 (tttt) cc_final: 0.9401 (tttt) outliers start: 71 outliers final: 57 residues processed: 391 average time/residue: 0.2630 time to fit residues: 154.6752 Evaluate side-chains 408 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 554 SER Chi-restraints excluded: chain A residue 560 SER 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 609 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 650 SER 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 867 MET 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 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 454 TYR 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 604 ASN Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 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 783 LEU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 LEU 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 661 VAL Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.6980 chunk 148 optimal weight: 0.0870 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 B 605 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15625 Z= 0.210 Angle : 0.915 32.290 21074 Z= 0.404 Chirality : 0.066 1.694 2338 Planarity : 0.005 0.086 2526 Dihedral : 17.044 177.458 3373 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.59 % Favored : 89.30 % Rotamer: Outliers : 4.07 % Allowed : 23.84 % 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: -0.68 (0.21), residues: 1776 helix: 1.33 (0.18), residues: 946 sheet: -2.22 (0.52), residues: 86 loop : -2.74 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 589 HIS 0.005 0.001 HIS C 593 PHE 0.017 0.001 PHE D 476 TYR 0.030 0.002 TYR D 590 ARG 0.005 0.000 ARG D 431 *********************** 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 429 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 366 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: A 471 SER cc_start: 0.8777 (t) cc_final: 0.8441 (p) REVERT: A 487 LYS cc_start: 0.9269 (mtpp) cc_final: 0.8823 (mtmm) REVERT: A 665 GLU cc_start: 0.8905 (tp30) cc_final: 0.8638 (tm-30) REVERT: A 705 MET cc_start: 0.9568 (mtp) cc_final: 0.9165 (mtp) REVERT: A 770 MET cc_start: 0.9069 (tpp) cc_final: 0.8484 (tpp) REVERT: A 788 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: A 864 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 441 GLU cc_start: 0.8897 (tp30) cc_final: 0.8565 (tp30) REVERT: B 465 ASP cc_start: 0.9081 (m-30) cc_final: 0.8672 (m-30) REVERT: B 504 GLU cc_start: 0.8218 (pt0) cc_final: 0.7989 (pm20) REVERT: B 528 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7090 (t0) REVERT: B 603 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 658 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8817 (m-10) REVERT: B 686 GLU cc_start: 0.8726 (tt0) cc_final: 0.8269 (tm-30) REVERT: B 691 MET cc_start: 0.8649 (ptm) cc_final: 0.8432 (ptt) REVERT: B 779 THR cc_start: 0.9458 (m) cc_final: 0.9232 (p) REVERT: B 793 MET cc_start: 0.9390 (tpp) cc_final: 0.9115 (mmm) REVERT: B 796 GLU cc_start: 0.9366 (tp30) cc_final: 0.9088 (tp30) REVERT: B 797 LYS cc_start: 0.9729 (tttt) cc_final: 0.9408 (tttp) REVERT: C 457 ASP cc_start: 0.9047 (t0) cc_final: 0.8710 (t0) REVERT: C 460 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: C 471 SER cc_start: 0.8920 (t) cc_final: 0.8509 (p) REVERT: C 487 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8746 (mtmm) REVERT: C 593 HIS cc_start: 0.8825 (m90) cc_final: 0.8503 (m90) REVERT: C 603 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6956 (mm-30) REVERT: C 691 MET cc_start: 0.9158 (ptp) cc_final: 0.8830 (ptt) REVERT: C 705 MET cc_start: 0.9684 (mtp) cc_final: 0.9206 (mtp) REVERT: C 709 MET cc_start: 0.9295 (mtp) cc_final: 0.8708 (mtm) REVERT: C 723 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8603 (mt-10) REVERT: C 754 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8609 (tm-30) REVERT: C 864 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 441 GLU cc_start: 0.8849 (tp30) cc_final: 0.8454 (tp30) REVERT: D 504 GLU cc_start: 0.7544 (mp0) cc_final: 0.7256 (mp0) REVERT: D 528 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7300 (t70) REVERT: D 603 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 686 GLU cc_start: 0.8718 (tt0) cc_final: 0.8158 (tm-30) REVERT: D 687 ASP cc_start: 0.8823 (m-30) cc_final: 0.7693 (m-30) REVERT: D 691 MET cc_start: 0.8557 (ptm) cc_final: 0.8332 (ptt) REVERT: D 784 GLN cc_start: 0.9236 (tt0) cc_final: 0.8898 (tm-30) REVERT: D 788 GLU cc_start: 0.8998 (mp0) cc_final: 0.8677 (mp0) REVERT: D 793 MET cc_start: 0.9258 (mmt) cc_final: 0.9016 (mmm) REVERT: D 797 LYS cc_start: 0.9694 (tttt) cc_final: 0.9396 (tttt) outliers start: 63 outliers final: 50 residues processed: 396 average time/residue: 0.2549 time to fit residues: 152.8052 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 355 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 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 750 CYS Chi-restraints excluded: chain A residue 755 ILE 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 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 658 PHE 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 454 TYR 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 604 ASN Chi-restraints excluded: chain C residue 605 ASN 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 783 LEU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 LEU 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 167 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 116 optimal weight: 0.0970 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15625 Z= 0.232 Angle : 0.924 32.488 21074 Z= 0.411 Chirality : 0.066 1.685 2338 Planarity : 0.005 0.087 2526 Dihedral : 16.806 175.589 3373 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.42 % Favored : 89.53 % Rotamer: Outliers : 4.20 % Allowed : 24.16 % Favored : 71.64 % 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: -0.65 (0.21), residues: 1776 helix: 1.37 (0.18), residues: 948 sheet: -2.18 (0.52), residues: 86 loop : -2.77 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 589 HIS 0.004 0.001 HIS A 593 PHE 0.017 0.001 PHE D 842 TYR 0.029 0.002 TYR D 590 ARG 0.004 0.000 ARG A 800 ********************** 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 426 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 361 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: A 471 SER cc_start: 0.8779 (t) cc_final: 0.8463 (p) REVERT: A 487 LYS cc_start: 0.9257 (mtpp) cc_final: 0.8909 (mtmm) REVERT: A 665 GLU cc_start: 0.8894 (tp30) cc_final: 0.8644 (tm-30) REVERT: A 681 GLU cc_start: 0.7975 (pm20) cc_final: 0.7742 (pm20) REVERT: A 705 MET cc_start: 0.9584 (mtp) cc_final: 0.9140 (mtp) REVERT: A 719 LYS cc_start: 0.8562 (tppt) cc_final: 0.8143 (tppt) REVERT: A 770 MET cc_start: 0.9040 (tpp) cc_final: 0.8479 (tpp) REVERT: A 788 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: A 864 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 869 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8133 (pp) REVERT: B 441 GLU cc_start: 0.8889 (tp30) cc_final: 0.8594 (tp30) REVERT: B 528 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7084 (t0) REVERT: B 603 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 658 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8842 (m-10) REVERT: B 686 GLU cc_start: 0.8748 (tt0) cc_final: 0.8278 (tm-30) REVERT: B 691 MET cc_start: 0.8633 (ptm) cc_final: 0.8416 (ptt) REVERT: B 779 THR cc_start: 0.9462 (m) cc_final: 0.9231 (p) REVERT: B 793 MET cc_start: 0.9392 (tpp) cc_final: 0.9132 (mmm) REVERT: B 797 LYS cc_start: 0.9733 (tttt) cc_final: 0.9436 (tttp) REVERT: C 457 ASP cc_start: 0.9070 (t0) cc_final: 0.8748 (t0) REVERT: C 460 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: C 471 SER cc_start: 0.8926 (t) cc_final: 0.8523 (p) REVERT: C 487 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8893 (mtmm) REVERT: C 593 HIS cc_start: 0.8825 (m90) cc_final: 0.8524 (m90) REVERT: C 603 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6949 (mm-30) REVERT: C 681 GLU cc_start: 0.8119 (pm20) cc_final: 0.7816 (pm20) REVERT: C 709 MET cc_start: 0.9313 (mtp) cc_final: 0.8723 (mtm) REVERT: C 723 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8592 (mt-10) REVERT: C 754 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8628 (tm-30) REVERT: C 864 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7647 (mt-10) REVERT: D 431 ARG cc_start: 0.9048 (ttp-110) cc_final: 0.8504 (ttp80) REVERT: D 441 GLU cc_start: 0.8897 (tp30) cc_final: 0.8512 (tp30) REVERT: D 504 GLU cc_start: 0.7515 (mp0) cc_final: 0.7240 (mp0) REVERT: D 528 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7263 (t70) REVERT: D 603 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 686 GLU cc_start: 0.8737 (tt0) cc_final: 0.8456 (tm-30) REVERT: D 691 MET cc_start: 0.8544 (ptm) cc_final: 0.8327 (ptt) REVERT: D 793 MET cc_start: 0.9260 (mmt) cc_final: 0.9021 (mmm) REVERT: D 797 LYS cc_start: 0.9687 (tttt) cc_final: 0.9404 (tttt) outliers start: 65 outliers final: 51 residues processed: 395 average time/residue: 0.2518 time to fit residues: 150.7761 Evaluate side-chains 407 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 560 SER 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 750 CYS Chi-restraints excluded: chain A residue 755 ILE 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 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 658 PHE 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 454 TYR 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 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 LEU 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 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 148 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 B 621 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103175 restraints weight = 25743.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107107 restraints weight = 12212.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109590 restraints weight = 8215.062| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15625 Z= 0.211 Angle : 0.910 32.568 21074 Z= 0.403 Chirality : 0.066 1.675 2338 Planarity : 0.005 0.084 2526 Dihedral : 16.622 177.149 3373 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.53 % Favored : 89.41 % Rotamer: Outliers : 3.94 % Allowed : 25.26 % Favored : 70.80 % 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: -0.58 (0.21), residues: 1776 helix: 1.42 (0.18), residues: 948 sheet: -2.16 (0.52), residues: 86 loop : -2.72 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 589 HIS 0.004 0.001 HIS C 593 PHE 0.015 0.001 PHE D 476 TYR 0.034 0.002 TYR C 733 ARG 0.003 0.000 ARG D 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.14 seconds wall clock time: 71 minutes 15.01 seconds (4275.01 seconds total)