Starting phenix.real_space_refine on Fri Jun 13 22:05:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxs_47297/06_2025/9dxs_47297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxs_47297/06_2025/9dxs_47297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxs_47297/06_2025/9dxs_47297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxs_47297/06_2025/9dxs_47297.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxs_47297/06_2025/9dxs_47297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxs_47297/06_2025/9dxs_47297.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 10002 2.51 5 N 2362 2.21 5 O 2818 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.39, per 1000 atoms: 0.68 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: 4.57 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: 1.60 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: 4.39 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2360 1.31 - 1.44: 4098 1.44 - 1.57: 8964 1.57 - 1.70: 47 1.70 - 1.82: 156 Bond restraints: 15625 Sorted by residual: bond pdb=" OAA 2J9 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAB 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" OAA 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.650 -0.198 2.00e-02 2.50e+03 9.75e+01 ... (remaining 15620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.52: 20918 6.52 - 13.03: 148 13.03 - 19.55: 0 19.55 - 26.07: 0 26.07 - 32.58: 8 Bond angle restraints: 21074 Sorted by residual: angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 150.25 -32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 D1002 " pdb=" CAN 2J9 D1002 " pdb=" NAO 2J9 D1002 " ideal model delta sigma weight residual 117.67 150.03 -32.36 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAH 2J9 B1001 " pdb=" CAN 2J9 B1001 " pdb=" NAO 2J9 B1001 " ideal model delta sigma weight residual 117.67 149.98 -32.31 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.64 -31.97 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.19 -31.37 3.00e+00 1.11e-01 1.09e+02 ... (remaining 21069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9600 35.97 - 71.94: 369 71.94 - 107.91: 86 107.91 - 143.88: 19 143.88 - 179.85: 6 Dihedral angle restraints: 10080 sinusoidal: 4928 harmonic: 5152 Sorted by residual: dihedral pdb=" CA GLU B 441 " pdb=" C GLU B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta harmonic sigma weight residual 180.00 -118.46 -61.54 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA GLU D 441 " pdb=" C GLU D 441 " pdb=" N PRO D 442 " pdb=" CA PRO D 442 " ideal model delta harmonic sigma weight residual -180.00 -118.46 -61.54 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA ASN A 819 " pdb=" C ASN A 819 " pdb=" N ILE A 820 " pdb=" CA ILE A 820 " ideal model delta harmonic sigma weight residual -180.00 -126.25 -53.75 0 5.00e+00 4.00e-02 1.16e+02 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 2332 1.059 - 2.119: 0 2.119 - 3.178: 4 3.178 - 4.237: 0 4.237 - 5.296: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" C13 CLR C1005 " pdb=" C12 CLR C1005 " pdb=" C14 CLR C1005 " pdb=" C17 CLR C1005 " both_signs ideal model delta sigma weight residual False -2.93 2.36 -5.30 2.00e-01 2.50e+01 7.01e+02 chirality pdb=" C13 CLR A1005 " pdb=" C12 CLR A1005 " pdb=" C14 CLR A1005 " pdb=" C17 CLR A1005 " both_signs ideal model delta sigma weight residual False -2.93 2.36 -5.29 2.00e-01 2.50e+01 6.99e+02 chirality pdb=" CAN 2J9 B1001 " pdb=" CAG 2J9 B1001 " pdb=" CAH 2J9 B1001 " pdb=" NAO 2J9 B1001 " both_signs ideal model delta sigma weight residual True 2.32 0.00 2.32 2.00e-01 2.50e+01 1.34e+02 ... (remaining 2335 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 441 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO D 442 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 442 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 442 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 441 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO B 442 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 515 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO A 516 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.040 5.00e-02 4.00e+02 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2304 2.75 - 3.29: 13969 3.29 - 3.83: 23421 3.83 - 4.36: 27480 4.36 - 4.90: 46583 Nonbonded interactions: 113757 Sorted by model distance: nonbonded pdb=" O VAL A 716 " pdb=" OH TYR A 733 " model vdw 2.217 3.040 nonbonded pdb=" O VAL C 716 " pdb=" OH TYR C 733 " model vdw 2.217 3.040 nonbonded pdb=" ND1 HIS A 593 " pdb=" O PRO D 594 " model vdw 2.298 3.120 nonbonded pdb=" OH TYR C 590 " pdb=" OD1 ASN C 605 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 590 " pdb=" OD1 ASN A 605 " model vdw 2.321 3.040 ... (remaining 113752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'B' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'C' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'D' and (resid 429 through 874 or resid 1003 or resid 1005)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.830 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.202 15648 Z= 0.541 Angle : 1.517 32.584 21138 Z= 0.656 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01958 ( 8) link_NAG-ASN : angle 9.99767 ( 24) link_BETA1-4 : bond 0.01894 ( 8) link_BETA1-4 : angle 6.01405 ( 24) hydrogen bonds : bond 0.31418 ( 602) hydrogen bonds : angle 9.30255 ( 1764) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.06836 ( 10) link_BETA1-3 : bond 0.02355 ( 2) link_BETA1-3 : angle 4.17187 ( 6) covalent geometry : bond 0.01124 (15625) covalent geometry : angle 1.46588 (21074) *********************** 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 : 1.513 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: 0.2803 time to fit residues: 260.0710 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 : 1.509 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.8380 ------------------------------------------------------------------------------- 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 456 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109648 restraints weight = 26449.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113678 restraints weight = 12124.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116225 restraints weight = 7998.102| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15648 Z= 0.173 Angle : 1.000 32.267 21138 Z= 0.444 Chirality : 0.067 1.703 2338 Planarity : 0.006 0.078 2526 Dihedral : 21.733 168.779 3373 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.70 % Favored : 89.08 % Rotamer: Outliers : 4.13 % Allowed : 13.95 % Favored : 81.91 % 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: -3.22 (0.17), residues: 1776 helix: -1.05 (0.15), residues: 932 sheet: -2.76 (0.50), residues: 100 loop : -3.52 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 589 HIS 0.003 0.001 HIS C 593 PHE 0.026 0.002 PHE B 529 TYR 0.026 0.002 TYR B 590 ARG 0.005 0.001 ARG C 800 Details of bonding type rmsd link_NAG-ASN : bond 0.01343 ( 8) link_NAG-ASN : angle 7.15785 ( 24) link_BETA1-4 : bond 0.01893 ( 8) link_BETA1-4 : angle 4.81479 ( 24) hydrogen bonds : bond 0.05983 ( 602) hydrogen bonds : angle 4.63948 ( 1764) SS BOND : bond 0.00992 ( 5) SS BOND : angle 1.26008 ( 10) link_BETA1-3 : bond 0.02383 ( 2) link_BETA1-3 : angle 3.69041 ( 6) covalent geometry : bond 0.00380 (15625) covalent geometry : angle 0.95582 (21074) *********************** 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 502 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 438 time to evaluate : 1.544 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 471 SER cc_start: 0.8853 (t) cc_final: 0.8542 (p) REVERT: A 487 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8790 (mtmm) REVERT: A 549 ASN cc_start: 0.9009 (t0) cc_final: 0.8779 (t0) REVERT: A 598 ASP cc_start: 0.8383 (m-30) cc_final: 0.8173 (m-30) REVERT: A 605 ASN cc_start: 0.8452 (m110) cc_final: 0.8197 (p0) REVERT: A 665 GLU cc_start: 0.8870 (tp30) cc_final: 0.8616 (tm-30) REVERT: A 673 ASP cc_start: 0.9185 (m-30) cc_final: 0.8706 (m-30) REVERT: A 705 MET cc_start: 0.9504 (mtp) cc_final: 0.9203 (mtp) REVERT: A 713 ARG cc_start: 0.8961 (ttt90) cc_final: 0.8735 (mtp-110) REVERT: A 775 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7924 (ttp-170) REVERT: A 795 LYS cc_start: 0.8944 (tttt) cc_final: 0.8664 (tttp) REVERT: B 465 ASP cc_start: 0.9031 (m-30) cc_final: 0.8829 (m-30) REVERT: B 473 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8793 (mp) REVERT: B 528 ASP cc_start: 0.7830 (m-30) cc_final: 0.7552 (m-30) REVERT: B 566 TYR cc_start: 0.9077 (m-10) cc_final: 0.8730 (m-80) REVERT: B 575 SER cc_start: 0.9270 (m) cc_final: 0.8873 (t) REVERT: B 603 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 611 SER cc_start: 0.9371 (m) cc_final: 0.8932 (m) REVERT: B 632 SER cc_start: 0.9539 (p) cc_final: 0.9290 (t) REVERT: B 662 GLU cc_start: 0.7728 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 668 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9207 (pp) REVERT: B 784 GLN cc_start: 0.9128 (tt0) cc_final: 0.8883 (tm-30) REVERT: B 795 LYS cc_start: 0.9473 (tttt) cc_final: 0.9145 (tptm) REVERT: B 797 LYS cc_start: 0.9709 (tttt) cc_final: 0.9431 (tttt) REVERT: B 798 TRP cc_start: 0.8994 (m100) cc_final: 0.8474 (m100) REVERT: B 844 TYR cc_start: 0.8971 (t80) cc_final: 0.8625 (t80) REVERT: B 861 MET cc_start: 0.8138 (tpt) cc_final: 0.7896 (tpp) REVERT: C 440 GLU cc_start: 0.8291 (tp30) cc_final: 0.7859 (tp30) REVERT: C 487 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8575 (mtmm) REVERT: C 488 TYR cc_start: 0.9019 (m-10) cc_final: 0.8684 (m-10) REVERT: C 565 MET cc_start: 0.7866 (tpt) cc_final: 0.7656 (mmt) REVERT: C 590 TYR cc_start: 0.8247 (p90) cc_final: 0.7705 (p90) REVERT: C 665 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 709 MET cc_start: 0.9330 (mtp) cc_final: 0.8546 (mtm) REVERT: C 748 ARG cc_start: 0.8350 (mmt90) cc_final: 0.7931 (mpt180) REVERT: D 465 ASP cc_start: 0.8896 (t0) cc_final: 0.8565 (t0) REVERT: D 575 SER cc_start: 0.9202 (m) cc_final: 0.8875 (t) REVERT: D 603 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8088 (mm-30) REVERT: D 662 GLU cc_start: 0.7615 (tm-30) cc_final: 0.6860 (tm-30) REVERT: D 664 MET cc_start: 0.8302 (pmm) cc_final: 0.7767 (pmm) REVERT: D 668 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9209 (pp) REVERT: D 797 LYS cc_start: 0.9676 (tttt) cc_final: 0.9307 (tttm) REVERT: D 798 TRP cc_start: 0.9205 (m100) cc_final: 0.8712 (m100) outliers start: 64 outliers final: 33 residues processed: 463 average time/residue: 0.2600 time to fit residues: 180.7344 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 375 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 668 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU 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 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 125 optimal weight: 0.0020 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 GLN C 593 HIS C 605 ASN C 677 GLN D 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105443 restraints weight = 25831.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109383 restraints weight = 11740.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111892 restraints weight = 7679.112| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15648 Z= 0.146 Angle : 0.939 31.821 21138 Z= 0.409 Chirality : 0.067 1.711 2338 Planarity : 0.005 0.077 2526 Dihedral : 20.175 172.909 3373 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.30 % Favored : 89.53 % Rotamer: Outliers : 4.39 % Allowed : 17.44 % Favored : 78.17 % 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: -2.16 (0.19), residues: 1776 helix: 0.01 (0.17), residues: 932 sheet: -2.63 (0.50), residues: 88 loop : -3.24 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 589 HIS 0.003 0.001 HIS A 593 PHE 0.022 0.001 PHE A 708 TYR 0.027 0.002 TYR A 733 ARG 0.004 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.01169 ( 8) link_NAG-ASN : angle 6.59602 ( 24) link_BETA1-4 : bond 0.01661 ( 8) link_BETA1-4 : angle 4.31256 ( 24) hydrogen bonds : bond 0.04654 ( 602) hydrogen bonds : angle 4.22543 ( 1764) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.98577 ( 10) link_BETA1-3 : bond 0.01571 ( 2) link_BETA1-3 : angle 2.87173 ( 6) covalent geometry : bond 0.00316 (15625) covalent geometry : angle 0.90082 (21074) *********************** 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 483 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 415 time to evaluate : 1.542 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: A 471 SER cc_start: 0.8817 (t) cc_final: 0.8495 (p) REVERT: A 487 LYS cc_start: 0.9177 (mtpp) cc_final: 0.8801 (mtmm) REVERT: A 549 ASN cc_start: 0.8920 (t0) cc_final: 0.8718 (t0) REVERT: A 665 GLU cc_start: 0.8880 (tp30) cc_final: 0.8624 (tm-30) REVERT: A 672 ASP cc_start: 0.8751 (p0) cc_final: 0.8521 (p0) REVERT: A 673 ASP cc_start: 0.8993 (m-30) cc_final: 0.8784 (m-30) REVERT: A 705 MET cc_start: 0.9524 (mtp) cc_final: 0.9085 (mtp) REVERT: A 795 LYS cc_start: 0.8922 (tttt) cc_final: 0.8638 (tttp) REVERT: B 473 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8661 (mp) REVERT: B 528 ASP cc_start: 0.7723 (m-30) cc_final: 0.7494 (m-30) REVERT: B 566 TYR cc_start: 0.9065 (m-10) cc_final: 0.8620 (m-80) REVERT: B 603 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 611 SER cc_start: 0.9439 (m) cc_final: 0.9039 (m) REVERT: B 726 GLN cc_start: 0.8949 (mm110) cc_final: 0.8728 (mm-40) REVERT: B 795 LYS cc_start: 0.9456 (tttt) cc_final: 0.9182 (tptm) REVERT: B 797 LYS cc_start: 0.9713 (tttt) cc_final: 0.9406 (tttt) REVERT: B 798 TRP cc_start: 0.9003 (m100) cc_final: 0.8476 (m100) REVERT: B 844 TYR cc_start: 0.8884 (t80) cc_final: 0.8679 (t80) REVERT: B 861 MET cc_start: 0.8119 (tpt) cc_final: 0.7876 (tpp) REVERT: C 440 GLU cc_start: 0.8290 (tp30) cc_final: 0.7937 (tp30) REVERT: C 457 ASP cc_start: 0.8880 (t0) cc_final: 0.8514 (t0) REVERT: C 471 SER cc_start: 0.8778 (t) cc_final: 0.8410 (p) REVERT: C 487 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8580 (mtmm) REVERT: C 488 TYR cc_start: 0.8970 (m-10) cc_final: 0.8624 (m-10) REVERT: C 498 TRP cc_start: 0.8888 (m100) cc_final: 0.8308 (m100) REVERT: C 565 MET cc_start: 0.7819 (tpt) cc_final: 0.7544 (mmt) REVERT: C 590 TYR cc_start: 0.8469 (p90) cc_final: 0.8020 (p90) REVERT: C 593 HIS cc_start: 0.8702 (m90) cc_final: 0.8414 (m90) REVERT: C 596 ASN cc_start: 0.8467 (t0) cc_final: 0.8258 (t0) REVERT: C 665 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8355 (tp30) REVERT: C 709 MET cc_start: 0.9338 (mtp) cc_final: 0.9126 (mtp) REVERT: C 722 GLU cc_start: 0.8327 (tp30) cc_final: 0.8125 (tp30) REVERT: C 754 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8753 (tm-30) REVERT: C 770 MET cc_start: 0.8950 (tpp) cc_final: 0.8482 (tpp) REVERT: D 504 GLU cc_start: 0.7256 (mp0) cc_final: 0.7043 (mp0) REVERT: D 575 SER cc_start: 0.9194 (m) cc_final: 0.8851 (t) REVERT: D 603 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7952 (mm-30) REVERT: D 668 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9207 (pp) REVERT: D 793 MET cc_start: 0.9173 (mmt) cc_final: 0.8909 (mmm) REVERT: D 797 LYS cc_start: 0.9650 (tttt) cc_final: 0.9411 (ttpp) REVERT: D 798 TRP cc_start: 0.9234 (m100) cc_final: 0.8946 (m100) outliers start: 68 outliers final: 45 residues processed: 444 average time/residue: 0.2471 time to fit residues: 165.9675 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 364 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL 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 819 ASN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 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 601 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 TYR 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 D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 668 ILE 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 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 34 optimal weight: 0.0060 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN B 604 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099282 restraints weight = 26149.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103027 restraints weight = 12445.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105406 restraints weight = 8405.652| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15648 Z= 0.247 Angle : 0.967 32.045 21138 Z= 0.425 Chirality : 0.068 1.693 2338 Planarity : 0.005 0.077 2526 Dihedral : 19.186 172.647 3373 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.43 % Favored : 88.46 % Rotamer: Outliers : 5.75 % Allowed : 18.35 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1776 helix: 0.44 (0.17), residues: 942 sheet: -2.99 (0.42), residues: 118 loop : -3.14 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 589 HIS 0.005 0.001 HIS C 593 PHE 0.015 0.002 PHE D 476 TYR 0.024 0.002 TYR B 590 ARG 0.004 0.000 ARG C 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00917 ( 8) link_NAG-ASN : angle 6.12120 ( 24) link_BETA1-4 : bond 0.01565 ( 8) link_BETA1-4 : angle 4.38191 ( 24) hydrogen bonds : bond 0.04501 ( 602) hydrogen bonds : angle 4.31800 ( 1764) SS BOND : bond 0.01268 ( 5) SS BOND : angle 1.06346 ( 10) link_BETA1-3 : bond 0.01298 ( 2) link_BETA1-3 : angle 2.48645 ( 6) covalent geometry : bond 0.00574 (15625) covalent geometry : angle 0.93341 (21074) *********************** 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 463 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 374 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 487 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8831 (mtmm) REVERT: A 491 GLN cc_start: 0.9472 (tt0) cc_final: 0.9169 (tt0) REVERT: A 665 GLU cc_start: 0.8886 (tp30) cc_final: 0.8625 (tm-30) REVERT: A 672 ASP cc_start: 0.8931 (p0) cc_final: 0.8571 (p0) REVERT: A 673 ASP cc_start: 0.9093 (m-30) cc_final: 0.8874 (m-30) REVERT: A 705 MET cc_start: 0.9552 (mtp) cc_final: 0.9103 (mtp) REVERT: A 867 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7891 (ttm) REVERT: A 869 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8387 (tt) REVERT: B 465 ASP cc_start: 0.9035 (m-30) cc_final: 0.8718 (m-30) REVERT: B 473 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 528 ASP cc_start: 0.7838 (m-30) cc_final: 0.7494 (m-30) REVERT: B 566 TYR cc_start: 0.9140 (m-10) cc_final: 0.8667 (m-80) REVERT: B 590 TYR cc_start: 0.8867 (p90) cc_final: 0.8419 (p90) REVERT: B 611 SER cc_start: 0.9401 (m) cc_final: 0.9164 (m) REVERT: B 620 MET cc_start: 0.9209 (mmm) cc_final: 0.8191 (mmm) REVERT: B 797 LYS cc_start: 0.9735 (tttt) cc_final: 0.9452 (tttt) REVERT: B 861 MET cc_start: 0.8131 (tpt) cc_final: 0.7896 (tpp) REVERT: C 457 ASP cc_start: 0.8928 (t0) cc_final: 0.8620 (t0) REVERT: C 460 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: C 471 SER cc_start: 0.8810 (t) cc_final: 0.8439 (p) REVERT: C 590 TYR cc_start: 0.8651 (p90) cc_final: 0.8308 (p90) REVERT: C 593 HIS cc_start: 0.8811 (m90) cc_final: 0.8502 (m90) REVERT: C 596 ASN cc_start: 0.8581 (t0) cc_final: 0.8298 (t0) REVERT: C 603 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7201 (mm-30) REVERT: C 665 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8393 (tp30) REVERT: C 705 MET cc_start: 0.9657 (mtp) cc_final: 0.9095 (mtp) REVERT: C 709 MET cc_start: 0.9399 (mtp) cc_final: 0.9128 (mtp) REVERT: C 754 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8528 (tm-30) REVERT: C 770 MET cc_start: 0.8939 (tpp) cc_final: 0.8530 (tpp) REVERT: C 864 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 504 GLU cc_start: 0.7370 (mp0) cc_final: 0.7154 (mp0) REVERT: D 528 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: D 575 SER cc_start: 0.9263 (m) cc_final: 0.8887 (t) REVERT: D 603 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8063 (mm-30) REVERT: D 662 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6443 (tm-30) REVERT: D 668 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9257 (pp) REVERT: D 793 MET cc_start: 0.9204 (mmt) cc_final: 0.8952 (mmm) REVERT: D 798 TRP cc_start: 0.9286 (m100) cc_final: 0.8858 (m100) outliers start: 89 outliers final: 64 residues processed: 421 average time/residue: 0.2377 time to fit residues: 151.9177 Evaluate side-chains 413 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 342 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU 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 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 A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 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 B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 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 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 677 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100341 restraints weight = 26065.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104194 restraints weight = 12277.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106656 restraints weight = 8229.982| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15648 Z= 0.152 Angle : 0.920 32.041 21138 Z= 0.398 Chirality : 0.066 1.692 2338 Planarity : 0.005 0.083 2526 Dihedral : 18.478 174.965 3373 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.53 % Favored : 89.36 % Rotamer: Outliers : 5.10 % Allowed : 20.28 % Favored : 74.61 % 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: -1.36 (0.20), residues: 1776 helix: 0.77 (0.17), residues: 942 sheet: -2.58 (0.49), residues: 86 loop : -3.03 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 589 HIS 0.005 0.001 HIS C 593 PHE 0.017 0.001 PHE B 476 TYR 0.017 0.002 TYR B 590 ARG 0.004 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00977 ( 8) link_NAG-ASN : angle 5.86679 ( 24) link_BETA1-4 : bond 0.01660 ( 8) link_BETA1-4 : angle 4.34533 ( 24) hydrogen bonds : bond 0.03970 ( 602) hydrogen bonds : angle 4.01409 ( 1764) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.90243 ( 10) link_BETA1-3 : bond 0.01258 ( 2) link_BETA1-3 : angle 2.15729 ( 6) covalent geometry : bond 0.00346 (15625) covalent geometry : angle 0.88716 (21074) *********************** 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 460 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 381 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: A 471 SER cc_start: 0.8819 (t) cc_final: 0.8540 (p) REVERT: A 487 LYS cc_start: 0.9217 (mtpp) cc_final: 0.8794 (mtmm) REVERT: A 528 ASP cc_start: 0.7610 (m-30) cc_final: 0.7298 (m-30) REVERT: A 585 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9118 (t) REVERT: A 665 GLU cc_start: 0.8869 (tp30) cc_final: 0.8601 (tm-30) REVERT: A 705 MET cc_start: 0.9532 (mtp) cc_final: 0.9056 (mtp) REVERT: A 770 MET cc_start: 0.8911 (tpp) cc_final: 0.8402 (tpp) REVERT: A 867 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7798 (ttm) REVERT: A 869 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8421 (tt) REVERT: B 465 ASP cc_start: 0.8982 (m-30) cc_final: 0.8762 (m-30) REVERT: B 528 ASP cc_start: 0.7779 (m-30) cc_final: 0.7534 (m-30) REVERT: B 566 TYR cc_start: 0.9115 (m-10) cc_final: 0.8656 (m-80) REVERT: B 611 SER cc_start: 0.9483 (m) cc_final: 0.9259 (m) REVERT: B 620 MET cc_start: 0.9152 (mmm) cc_final: 0.8140 (mmm) REVERT: B 770 MET cc_start: 0.8601 (tpp) cc_final: 0.8398 (tpp) REVERT: B 797 LYS cc_start: 0.9718 (tttt) cc_final: 0.9474 (tttt) REVERT: C 457 ASP cc_start: 0.8875 (t0) cc_final: 0.8547 (t0) REVERT: C 460 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: C 471 SER cc_start: 0.8772 (t) cc_final: 0.8391 (p) REVERT: C 590 TYR cc_start: 0.8674 (p90) cc_final: 0.8364 (p90) REVERT: C 593 HIS cc_start: 0.8736 (m90) cc_final: 0.8403 (m90) REVERT: C 596 ASN cc_start: 0.8592 (t0) cc_final: 0.8293 (t0) REVERT: C 603 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 665 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8349 (tp30) REVERT: C 681 GLU cc_start: 0.8241 (pm20) cc_final: 0.7867 (pm20) REVERT: C 705 MET cc_start: 0.9628 (mtp) cc_final: 0.9366 (mtp) REVERT: C 709 MET cc_start: 0.9376 (mtp) cc_final: 0.9076 (mtp) REVERT: C 722 GLU cc_start: 0.8520 (tp30) cc_final: 0.8198 (tp30) REVERT: C 754 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8735 (tm-30) REVERT: D 528 ASP cc_start: 0.7784 (m-30) cc_final: 0.7501 (m-30) REVERT: D 575 SER cc_start: 0.9238 (m) cc_final: 0.8846 (t) REVERT: D 603 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8021 (mm-30) REVERT: D 611 SER cc_start: 0.9528 (m) cc_final: 0.9240 (m) REVERT: D 668 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9229 (pp) REVERT: D 687 ASP cc_start: 0.8196 (m-30) cc_final: 0.7805 (m-30) REVERT: D 793 MET cc_start: 0.9159 (mmt) cc_final: 0.8905 (mmm) REVERT: D 797 LYS cc_start: 0.9662 (tttt) cc_final: 0.9297 (tttp) REVERT: D 798 TRP cc_start: 0.9277 (m100) cc_final: 0.8881 (m100) outliers start: 79 outliers final: 55 residues processed: 418 average time/residue: 0.2535 time to fit residues: 164.4657 Evaluate side-chains 403 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 342 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 609 LEU 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 A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 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 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 120 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102181 restraints weight = 25911.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106071 restraints weight = 12087.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108524 restraints weight = 8062.680| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15648 Z= 0.139 Angle : 0.919 32.298 21138 Z= 0.396 Chirality : 0.065 1.673 2338 Planarity : 0.005 0.094 2526 Dihedral : 17.929 176.871 3373 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.42 % Favored : 89.47 % Rotamer: Outliers : 5.43 % Allowed : 20.74 % Favored : 73.84 % 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: -1.14 (0.20), residues: 1776 helix: 1.00 (0.17), residues: 946 sheet: -2.70 (0.45), residues: 106 loop : -2.97 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 589 HIS 0.005 0.001 HIS A 593 PHE 0.014 0.001 PHE D 842 TYR 0.019 0.002 TYR D 590 ARG 0.003 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00937 ( 8) link_NAG-ASN : angle 5.58606 ( 24) link_BETA1-4 : bond 0.01649 ( 8) link_BETA1-4 : angle 4.44304 ( 24) hydrogen bonds : bond 0.03668 ( 602) hydrogen bonds : angle 3.85217 ( 1764) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.96760 ( 10) link_BETA1-3 : bond 0.01256 ( 2) link_BETA1-3 : angle 1.85475 ( 6) covalent geometry : bond 0.00317 (15625) covalent geometry : angle 0.88767 (21074) *********************** 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 453 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 1.780 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: 0.8362 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: A 471 SER cc_start: 0.8799 (t) cc_final: 0.8523 (p) REVERT: A 487 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8814 (mtmm) REVERT: A 528 ASP cc_start: 0.7587 (m-30) cc_final: 0.7300 (m-30) REVERT: A 585 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.9140 (t) REVERT: A 590 TYR cc_start: 0.8685 (p90) cc_final: 0.8230 (p90) REVERT: A 665 GLU cc_start: 0.8851 (tp30) cc_final: 0.8568 (tm-30) REVERT: A 691 MET cc_start: 0.8856 (ptt) cc_final: 0.8605 (ptt) REVERT: A 705 MET cc_start: 0.9511 (mtp) cc_final: 0.9093 (mtp) REVERT: A 770 MET cc_start: 0.8886 (tpp) cc_final: 0.8407 (tpp) REVERT: A 788 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: A 867 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7764 (ttm) REVERT: A 869 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 476 PHE cc_start: 0.7802 (p90) cc_final: 0.7597 (p90) REVERT: B 603 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 620 MET cc_start: 0.9139 (mmm) cc_final: 0.8184 (mmm) REVERT: B 793 MET cc_start: 0.9097 (mmt) cc_final: 0.8857 (mmm) REVERT: B 797 LYS cc_start: 0.9691 (tttt) cc_final: 0.9434 (tttt) REVERT: C 457 ASP cc_start: 0.8851 (t0) cc_final: 0.8545 (t0) REVERT: C 460 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: C 471 SER cc_start: 0.8735 (t) cc_final: 0.8337 (p) REVERT: C 590 TYR cc_start: 0.8674 (p90) cc_final: 0.8410 (p90) REVERT: C 593 HIS cc_start: 0.8721 (m90) cc_final: 0.8396 (m90) REVERT: C 596 ASN cc_start: 0.8598 (t0) cc_final: 0.8292 (t0) REVERT: C 603 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7289 (mm-30) REVERT: C 665 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8330 (tp30) REVERT: C 681 GLU cc_start: 0.8177 (pm20) cc_final: 0.7873 (pm20) REVERT: C 709 MET cc_start: 0.9351 (mtp) cc_final: 0.9092 (mtp) REVERT: C 722 GLU cc_start: 0.8403 (tp30) cc_final: 0.8126 (tp30) REVERT: C 723 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8570 (pt0) REVERT: C 754 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 864 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7434 (mt-10) REVERT: D 603 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8045 (mm-30) REVERT: D 668 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9220 (pp) REVERT: D 687 ASP cc_start: 0.8374 (m-30) cc_final: 0.7958 (m-30) REVERT: D 793 MET cc_start: 0.9128 (mmt) cc_final: 0.8883 (mmm) REVERT: D 797 LYS cc_start: 0.9629 (tttt) cc_final: 0.9317 (tttp) outliers start: 84 outliers final: 52 residues processed: 411 average time/residue: 0.2344 time to fit residues: 148.2676 Evaluate side-chains 410 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 351 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 585 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 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL 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 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100900 restraints weight = 25960.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104752 restraints weight = 12198.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107149 restraints weight = 8188.714| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15648 Z= 0.165 Angle : 0.926 32.274 21138 Z= 0.402 Chirality : 0.066 1.666 2338 Planarity : 0.005 0.087 2526 Dihedral : 17.551 177.151 3373 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.70 % Favored : 89.19 % Rotamer: Outliers : 5.30 % Allowed : 22.03 % Favored : 72.67 % 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: -0.94 (0.21), residues: 1776 helix: 1.16 (0.17), residues: 944 sheet: -2.56 (0.45), residues: 106 loop : -2.87 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 589 HIS 0.004 0.001 HIS A 593 PHE 0.014 0.001 PHE D 842 TYR 0.034 0.002 TYR D 590 ARG 0.004 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 8) link_NAG-ASN : angle 5.34709 ( 24) link_BETA1-4 : bond 0.01631 ( 8) link_BETA1-4 : angle 4.50450 ( 24) hydrogen bonds : bond 0.03697 ( 602) hydrogen bonds : angle 3.84432 ( 1764) SS BOND : bond 0.00316 ( 5) SS BOND : angle 1.04586 ( 10) link_BETA1-3 : bond 0.01244 ( 2) link_BETA1-3 : angle 1.66644 ( 6) covalent geometry : bond 0.00381 (15625) covalent geometry : angle 0.89582 (21074) *********************** 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 441 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 359 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 487 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8828 (mtmm) REVERT: A 528 ASP cc_start: 0.7618 (m-30) cc_final: 0.7325 (m-30) REVERT: A 585 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9115 (t) REVERT: A 590 TYR cc_start: 0.8685 (p90) cc_final: 0.8263 (p90) REVERT: A 665 GLU cc_start: 0.8852 (tp30) cc_final: 0.8574 (tm-30) REVERT: A 691 MET cc_start: 0.8890 (ptt) cc_final: 0.8522 (ptt) REVERT: A 705 MET cc_start: 0.9513 (mtp) cc_final: 0.9068 (mtp) REVERT: A 722 GLU cc_start: 0.8424 (tp30) cc_final: 0.8037 (tp30) REVERT: A 770 MET cc_start: 0.8873 (tpp) cc_final: 0.8395 (tpp) REVERT: A 788 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: A 869 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8383 (tt) REVERT: B 441 GLU cc_start: 0.8793 (tp30) cc_final: 0.8282 (tp30) REVERT: B 528 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7389 (t70) REVERT: B 588 GLU cc_start: 0.9480 (tp30) cc_final: 0.9276 (tp30) REVERT: B 620 MET cc_start: 0.9148 (mmm) cc_final: 0.8133 (mmm) REVERT: B 793 MET cc_start: 0.9102 (mmt) cc_final: 0.8862 (mmm) REVERT: B 795 LYS cc_start: 0.9452 (tptm) cc_final: 0.8844 (tptp) REVERT: B 797 LYS cc_start: 0.9707 (tttt) cc_final: 0.9463 (tttt) REVERT: C 457 ASP cc_start: 0.8825 (t0) cc_final: 0.8532 (t0) REVERT: C 460 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: C 471 SER cc_start: 0.8769 (t) cc_final: 0.8459 (p) REVERT: C 590 TYR cc_start: 0.8718 (p90) cc_final: 0.8496 (p90) REVERT: C 593 HIS cc_start: 0.8762 (m90) cc_final: 0.8445 (m90) REVERT: C 596 ASN cc_start: 0.8619 (t0) cc_final: 0.8330 (t0) REVERT: C 603 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 665 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8342 (tp30) REVERT: C 681 GLU cc_start: 0.8174 (pm20) cc_final: 0.7850 (pm20) REVERT: C 705 MET cc_start: 0.9605 (mtp) cc_final: 0.9151 (mtp) REVERT: C 709 MET cc_start: 0.9333 (mtp) cc_final: 0.9034 (mtp) REVERT: C 722 GLU cc_start: 0.8447 (tp30) cc_final: 0.8168 (tp30) REVERT: C 723 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8581 (pt0) REVERT: C 754 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 575 SER cc_start: 0.9211 (m) cc_final: 0.8804 (t) REVERT: D 603 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 793 MET cc_start: 0.9129 (mmt) cc_final: 0.8891 (mmm) REVERT: D 797 LYS cc_start: 0.9658 (tttt) cc_final: 0.9391 (tttt) REVERT: D 798 TRP cc_start: 0.9259 (m100) cc_final: 0.8831 (m100) outliers start: 82 outliers final: 61 residues processed: 399 average time/residue: 0.2321 time to fit residues: 142.1704 Evaluate side-chains 408 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 341 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 585 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 660 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 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 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 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 783 LEU 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 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** B 456 ASN C 621 GLN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104104 restraints weight = 25687.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108029 restraints weight = 11708.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110499 restraints weight = 7735.610| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15648 Z= 0.137 Angle : 0.913 32.299 21138 Z= 0.395 Chirality : 0.066 1.680 2338 Planarity : 0.005 0.085 2526 Dihedral : 17.202 178.180 3373 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.64 % Favored : 89.30 % Rotamer: Outliers : 4.72 % Allowed : 22.48 % Favored : 72.80 % 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: -0.81 (0.21), residues: 1776 helix: 1.25 (0.18), residues: 952 sheet: -2.45 (0.46), residues: 106 loop : -2.83 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 589 HIS 0.004 0.001 HIS C 593 PHE 0.019 0.001 PHE D 446 TYR 0.030 0.002 TYR D 590 ARG 0.004 0.000 ARG C 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 8) link_NAG-ASN : angle 5.11404 ( 24) link_BETA1-4 : bond 0.01634 ( 8) link_BETA1-4 : angle 4.55593 ( 24) hydrogen bonds : bond 0.03445 ( 602) hydrogen bonds : angle 3.74982 ( 1764) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.96743 ( 10) link_BETA1-3 : bond 0.01258 ( 2) link_BETA1-3 : angle 1.58345 ( 6) covalent geometry : bond 0.00310 (15625) covalent geometry : angle 0.88403 (21074) *********************** 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 437 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 364 time to evaluate : 1.683 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: 0.8371 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: A 487 LYS cc_start: 0.9152 (mtpp) cc_final: 0.8742 (mtmm) REVERT: A 528 ASP cc_start: 0.7650 (m-30) cc_final: 0.7323 (m-30) REVERT: A 585 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8999 (t) REVERT: A 590 TYR cc_start: 0.8789 (p90) cc_final: 0.8405 (p90) REVERT: A 665 GLU cc_start: 0.8893 (tp30) cc_final: 0.8625 (tm-30) REVERT: A 691 MET cc_start: 0.8923 (ptt) cc_final: 0.8689 (ptt) REVERT: A 705 MET cc_start: 0.9568 (mtp) cc_final: 0.9144 (mtp) REVERT: A 770 MET cc_start: 0.8956 (tpp) cc_final: 0.8402 (tpp) REVERT: A 788 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 869 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 441 GLU cc_start: 0.8836 (tp30) cc_final: 0.8412 (tp30) REVERT: B 528 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7103 (t0) REVERT: B 588 GLU cc_start: 0.9458 (tp30) cc_final: 0.9242 (tp30) REVERT: B 603 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 620 MET cc_start: 0.9188 (mmm) cc_final: 0.8088 (mmm) REVERT: B 793 MET cc_start: 0.9157 (mmt) cc_final: 0.8921 (mmm) REVERT: B 795 LYS cc_start: 0.9449 (tptm) cc_final: 0.8825 (tptp) REVERT: B 797 LYS cc_start: 0.9706 (tttt) cc_final: 0.9415 (tttp) REVERT: C 457 ASP cc_start: 0.8932 (t0) cc_final: 0.8631 (t0) REVERT: C 460 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: C 471 SER cc_start: 0.8893 (t) cc_final: 0.8505 (p) REVERT: C 593 HIS cc_start: 0.8808 (m90) cc_final: 0.8468 (m90) REVERT: C 596 ASN cc_start: 0.8699 (t0) cc_final: 0.8413 (t0) REVERT: C 603 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7244 (mm-30) REVERT: C 681 GLU cc_start: 0.8231 (pm20) cc_final: 0.7916 (pm20) REVERT: C 705 MET cc_start: 0.9642 (mtp) cc_final: 0.9341 (mtp) REVERT: C 709 MET cc_start: 0.9367 (mtp) cc_final: 0.9059 (mtp) REVERT: C 722 GLU cc_start: 0.8497 (tp30) cc_final: 0.8166 (tp30) REVERT: C 754 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8721 (tm-30) REVERT: D 575 SER cc_start: 0.9189 (m) cc_final: 0.8765 (t) REVERT: D 603 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 691 MET cc_start: 0.8512 (ptm) cc_final: 0.8278 (ptt) REVERT: D 793 MET cc_start: 0.9169 (mmt) cc_final: 0.8934 (mmm) REVERT: D 797 LYS cc_start: 0.9671 (tttt) cc_final: 0.9405 (tttt) REVERT: D 798 TRP cc_start: 0.9254 (m100) cc_final: 0.8838 (m100) outliers start: 73 outliers final: 58 residues processed: 399 average time/residue: 0.2624 time to fit residues: 163.4856 Evaluate side-chains 409 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain 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 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 831 LEU Chi-restraints excluded: chain B residue 867 MET 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 605 ASN Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 867 MET 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 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 743 GLU 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 867 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100265 restraints weight = 25883.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104064 restraints weight = 12269.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106465 restraints weight = 8262.425| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15648 Z= 0.185 Angle : 0.947 32.346 21138 Z= 0.413 Chirality : 0.066 1.682 2338 Planarity : 0.005 0.085 2526 Dihedral : 16.969 175.518 3373 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.87 % Favored : 89.02 % 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: -0.81 (0.21), residues: 1776 helix: 1.31 (0.18), residues: 948 sheet: -2.75 (0.40), residues: 140 loop : -2.82 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 589 HIS 0.003 0.001 HIS C 593 PHE 0.014 0.001 PHE B 476 TYR 0.027 0.002 TYR D 590 ARG 0.004 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 8) link_NAG-ASN : angle 5.02525 ( 24) link_BETA1-4 : bond 0.01606 ( 8) link_BETA1-4 : angle 4.63273 ( 24) hydrogen bonds : bond 0.03682 ( 602) hydrogen bonds : angle 3.87967 ( 1764) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.90049 ( 10) link_BETA1-3 : bond 0.01142 ( 2) link_BETA1-3 : angle 1.56849 ( 6) covalent geometry : bond 0.00429 (15625) covalent geometry : angle 0.91962 (21074) *********************** 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 421 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 350 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 487 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8822 (mtmm) REVERT: A 528 ASP cc_start: 0.7638 (m-30) cc_final: 0.7322 (m-30) REVERT: A 585 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.9038 (t) REVERT: A 590 TYR cc_start: 0.8741 (p90) cc_final: 0.8292 (p90) REVERT: A 665 GLU cc_start: 0.8805 (tp30) cc_final: 0.8563 (tm-30) REVERT: A 691 MET cc_start: 0.8913 (ptt) cc_final: 0.8647 (ptt) REVERT: A 705 MET cc_start: 0.9532 (mtp) cc_final: 0.9124 (mtp) REVERT: A 770 MET cc_start: 0.8863 (tpp) cc_final: 0.8423 (tpp) REVERT: A 788 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: A 864 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7872 (mt-10) REVERT: A 869 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 441 GLU cc_start: 0.8789 (tp30) cc_final: 0.8424 (tp30) REVERT: B 528 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7240 (t0) REVERT: B 588 GLU cc_start: 0.9433 (tp30) cc_final: 0.9165 (tp30) REVERT: B 603 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7717 (mm-30) REVERT: B 620 MET cc_start: 0.9144 (mmm) cc_final: 0.8087 (mmm) REVERT: B 658 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8945 (m-10) REVERT: B 687 ASP cc_start: 0.8124 (m-30) cc_final: 0.7780 (m-30) REVERT: B 793 MET cc_start: 0.9130 (mmt) cc_final: 0.8904 (mmm) REVERT: B 795 LYS cc_start: 0.9466 (tptm) cc_final: 0.8850 (tptp) REVERT: B 797 LYS cc_start: 0.9684 (tttt) cc_final: 0.9428 (tttp) REVERT: C 457 ASP cc_start: 0.8791 (t0) cc_final: 0.8535 (t0) REVERT: C 460 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: C 471 SER cc_start: 0.8880 (t) cc_final: 0.8478 (p) REVERT: C 593 HIS cc_start: 0.8796 (m90) cc_final: 0.8501 (m90) REVERT: C 603 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7316 (mm-30) REVERT: C 681 GLU cc_start: 0.8180 (pm20) cc_final: 0.7915 (pm20) REVERT: C 705 MET cc_start: 0.9597 (mtp) cc_final: 0.9364 (mtp) REVERT: C 722 GLU cc_start: 0.8438 (tp30) cc_final: 0.8177 (tp30) REVERT: C 723 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8581 (pt0) REVERT: C 754 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8733 (tm-30) REVERT: C 864 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7484 (mt-10) REVERT: D 575 SER cc_start: 0.9235 (m) cc_final: 0.8854 (t) REVERT: D 576 CYS cc_start: 0.9127 (m) cc_final: 0.8471 (t) REVERT: D 603 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8075 (mm-30) REVERT: D 691 MET cc_start: 0.8551 (ptm) cc_final: 0.8335 (ptt) REVERT: D 793 MET cc_start: 0.9126 (mmt) cc_final: 0.8896 (mmm) REVERT: D 797 LYS cc_start: 0.9663 (tttt) cc_final: 0.9402 (tttt) outliers start: 71 outliers final: 59 residues processed: 385 average time/residue: 0.2350 time to fit residues: 138.8831 Evaluate side-chains 408 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 536 LEU 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 585 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 626 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 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 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 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 471 SER 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 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 742 ILE 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 867 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 175 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 677 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102607 restraints weight = 25958.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106516 restraints weight = 12165.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108974 restraints weight = 8144.308| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15648 Z= 0.141 Angle : 0.934 32.495 21138 Z= 0.406 Chirality : 0.066 1.673 2338 Planarity : 0.005 0.083 2526 Dihedral : 16.737 177.496 3373 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.47 % Favored : 89.47 % Rotamer: Outliers : 4.01 % Allowed : 24.16 % Favored : 71.83 % 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: 950 sheet: -2.10 (0.45), residues: 118 loop : -2.78 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 589 HIS 0.005 0.001 HIS C 593 PHE 0.014 0.001 PHE B 476 TYR 0.027 0.002 TYR D 590 ARG 0.006 0.000 ARG A 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00859 ( 8) link_NAG-ASN : angle 4.87359 ( 24) link_BETA1-4 : bond 0.01638 ( 8) link_BETA1-4 : angle 4.64380 ( 24) hydrogen bonds : bond 0.03412 ( 602) hydrogen bonds : angle 3.74422 ( 1764) SS BOND : bond 0.00255 ( 5) SS BOND : angle 1.01654 ( 10) link_BETA1-3 : bond 0.01129 ( 2) link_BETA1-3 : angle 1.54543 ( 6) covalent geometry : bond 0.00320 (15625) covalent geometry : angle 0.90728 (21074) ********************** 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 424 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 362 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: A 487 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8829 (mtmm) REVERT: A 528 ASP cc_start: 0.7646 (m-30) cc_final: 0.7317 (m-30) REVERT: A 585 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9011 (t) REVERT: A 590 TYR cc_start: 0.8713 (p90) cc_final: 0.8280 (p90) REVERT: A 665 GLU cc_start: 0.8816 (tp30) cc_final: 0.8567 (tm-30) REVERT: A 677 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8847 (tm-30) REVERT: A 681 GLU cc_start: 0.7913 (pm20) cc_final: 0.7616 (pm20) REVERT: A 691 MET cc_start: 0.8866 (ptt) cc_final: 0.8432 (ptt) REVERT: A 705 MET cc_start: 0.9508 (mtp) cc_final: 0.8791 (mtp) REVERT: A 709 MET cc_start: 0.9253 (mtp) cc_final: 0.8649 (mpp) REVERT: A 770 MET cc_start: 0.8875 (tpp) cc_final: 0.8434 (tpp) REVERT: A 788 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: A 864 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 869 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8414 (tt) REVERT: B 441 GLU cc_start: 0.8726 (tp30) cc_final: 0.8485 (tp30) REVERT: B 528 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7083 (t0) REVERT: B 588 GLU cc_start: 0.9397 (tp30) cc_final: 0.9097 (tp30) REVERT: B 603 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 620 MET cc_start: 0.9094 (mmm) cc_final: 0.8175 (mmm) REVERT: B 658 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8898 (m-10) REVERT: B 793 MET cc_start: 0.9100 (mmt) cc_final: 0.8873 (mmm) REVERT: B 795 LYS cc_start: 0.9472 (tptm) cc_final: 0.8844 (tptp) REVERT: B 797 LYS cc_start: 0.9678 (tttt) cc_final: 0.9436 (tttp) REVERT: C 457 ASP cc_start: 0.8784 (t0) cc_final: 0.8527 (t0) REVERT: C 460 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: C 471 SER cc_start: 0.8886 (t) cc_final: 0.8452 (p) REVERT: C 593 HIS cc_start: 0.8794 (m90) cc_final: 0.8500 (m90) REVERT: C 603 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 681 GLU cc_start: 0.8195 (pm20) cc_final: 0.7954 (pm20) REVERT: C 705 MET cc_start: 0.9585 (mtp) cc_final: 0.9149 (mtp) REVERT: C 722 GLU cc_start: 0.8428 (tp30) cc_final: 0.8215 (tp30) REVERT: C 723 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8572 (pt0) REVERT: C 754 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 864 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7487 (mt-10) REVERT: D 575 SER cc_start: 0.9200 (m) cc_final: 0.8834 (t) REVERT: D 603 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 793 MET cc_start: 0.9109 (mmt) cc_final: 0.8881 (mmm) REVERT: D 797 LYS cc_start: 0.9643 (tttt) cc_final: 0.9334 (tttp) outliers start: 62 outliers final: 50 residues processed: 392 average time/residue: 0.2544 time to fit residues: 153.1077 Evaluate side-chains 406 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 536 LEU 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 585 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 626 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain 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 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 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 601 VAL Chi-restraints excluded: chain C residue 602 VAL 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 867 MET 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 743 GLU 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 867 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 125 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 0.0010 chunk 117 optimal weight: 5.9990 overall best weight: 0.8088 ------------------------------------------------------------------------------- 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 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102333 restraints weight = 25739.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106155 restraints weight = 12256.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108569 restraints weight = 8258.605| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15648 Z= 0.150 Angle : 0.940 32.442 21138 Z= 0.410 Chirality : 0.066 1.682 2338 Planarity : 0.005 0.095 2526 Dihedral : 16.566 177.587 3373 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.75 % Favored : 89.19 % Rotamer: Outliers : 4.39 % Allowed : 24.55 % Favored : 71.06 % 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: -0.69 (0.21), residues: 1776 helix: 1.37 (0.18), residues: 948 sheet: -2.59 (0.41), residues: 140 loop : -2.73 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 589 HIS 0.004 0.001 HIS A 593 PHE 0.016 0.001 PHE B 446 TYR 0.027 0.002 TYR D 590 ARG 0.003 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 8) link_NAG-ASN : angle 4.77811 ( 24) link_BETA1-4 : bond 0.01621 ( 8) link_BETA1-4 : angle 4.64013 ( 24) hydrogen bonds : bond 0.03491 ( 602) hydrogen bonds : angle 3.77386 ( 1764) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.97773 ( 10) link_BETA1-3 : bond 0.01174 ( 2) link_BETA1-3 : angle 1.53891 ( 6) covalent geometry : bond 0.00345 (15625) covalent geometry : angle 0.91350 (21074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6077.82 seconds wall clock time: 106 minutes 34.60 seconds (6394.60 seconds total)