Starting phenix.real_space_refine on Wed Jan 14 10:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0f_42853/01_2026/8v0f_42853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0f_42853/01_2026/8v0f_42853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0f_42853/01_2026/8v0f_42853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0f_42853/01_2026/8v0f_42853.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0f_42853/01_2026/8v0f_42853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0f_42853/01_2026/8v0f_42853.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9363 2.51 5 N 2529 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2455 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2455 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2446 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2446 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Chain: "E" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2446 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Chain: "F" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2455 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Time building chain proxies: 3.20, per 1000 atoms: 0.22 Number of scatterers: 14703 At special positions: 0 Unit cell: (142.45, 131.45, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2745 8.00 N 2529 7.00 C 9363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 539.1 milliseconds 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3474 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 6 sheets defined 84.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 648 through 657 removed outlier: 3.958A pdb=" N ILE A 657 " --> pdb=" O TYR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.991A pdb=" N GLN A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 704 removed outlier: 3.717A pdb=" N LEU A 681 " --> pdb=" O PRO A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 717 Processing helix chain 'A' and resid 719 through 740 removed outlier: 3.843A pdb=" N THR A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 771 removed outlier: 3.731A pdb=" N ILE A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 787 through 799 removed outlier: 4.133A pdb=" N PHE A 791 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 829 removed outlier: 3.952A pdb=" N LEU A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.935A pdb=" N LYS A 859 " --> pdb=" O SER A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 872 removed outlier: 3.564A pdb=" N LYS A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 890 removed outlier: 3.627A pdb=" N LYS A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 915 removed outlier: 3.765A pdb=" N GLN A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 931 removed outlier: 3.810A pdb=" N ARG A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 635 Processing helix chain 'B' and resid 640 through 648 removed outlier: 3.829A pdb=" N GLU B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 656 Processing helix chain 'B' and resid 661 through 675 removed outlier: 3.967A pdb=" N GLN B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 704 removed outlier: 3.626A pdb=" N LEU B 681 " --> pdb=" O PRO B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 717 Processing helix chain 'B' and resid 719 through 739 removed outlier: 3.931A pdb=" N THR B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 743 through 771 removed outlier: 3.769A pdb=" N ILE B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 787 Processing helix chain 'B' and resid 787 through 799 removed outlier: 4.200A pdb=" N PHE B 791 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 798 " --> pdb=" O ALA B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 802 No H-bonds generated for 'chain 'B' and resid 800 through 802' Processing helix chain 'B' and resid 808 through 829 removed outlier: 3.942A pdb=" N LEU B 828 " --> pdb=" O ASP B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 846 Processing helix chain 'B' and resid 849 through 859 removed outlier: 3.925A pdb=" N LYS B 859 " --> pdb=" O SER B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 872 removed outlier: 3.603A pdb=" N LYS B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 889 removed outlier: 3.563A pdb=" N LYS B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 915 removed outlier: 3.535A pdb=" N GLN B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 931 removed outlier: 3.723A pdb=" N ARG B 925 " --> pdb=" O ASN B 921 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 635 Processing helix chain 'C' and resid 640 through 648 Processing helix chain 'C' and resid 648 through 657 removed outlier: 3.945A pdb=" N ILE C 657 " --> pdb=" O TYR C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 675 removed outlier: 4.132A pdb=" N GLN C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR C 672 " --> pdb=" O GLU C 668 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP C 673 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 704 removed outlier: 3.813A pdb=" N LEU C 681 " --> pdb=" O PRO C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 717 Processing helix chain 'C' and resid 719 through 739 removed outlier: 3.577A pdb=" N THR C 723 " --> pdb=" O GLY C 719 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 743 through 771 removed outlier: 3.653A pdb=" N ILE C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 787 Processing helix chain 'C' and resid 787 through 799 removed outlier: 4.265A pdb=" N PHE C 791 " --> pdb=" O THR C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 802 No H-bonds generated for 'chain 'C' and resid 800 through 802' Processing helix chain 'C' and resid 808 through 826 removed outlier: 3.662A pdb=" N TYR C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 846 Processing helix chain 'C' and resid 849 through 859 removed outlier: 3.638A pdb=" N LYS C 859 " --> pdb=" O SER C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 872 removed outlier: 3.927A pdb=" N ASN C 867 " --> pdb=" O ARG C 863 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 889 removed outlier: 3.644A pdb=" N LYS C 879 " --> pdb=" O GLU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 915 removed outlier: 3.829A pdb=" N TYR C 894 " --> pdb=" O GLN C 890 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 931 removed outlier: 3.654A pdb=" N ARG C 925 " --> pdb=" O ASN C 921 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 635 removed outlier: 3.566A pdb=" N SER D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 628 " --> pdb=" O ASP D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 648 removed outlier: 4.025A pdb=" N THR D 646 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 657 removed outlier: 3.534A pdb=" N GLU D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 657 " --> pdb=" O TYR D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 675 removed outlier: 3.967A pdb=" N GLN D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR D 672 " --> pdb=" O GLU D 668 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TRP D 673 " --> pdb=" O ALA D 669 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 703 removed outlier: 3.689A pdb=" N LEU D 681 " --> pdb=" O PRO D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 717 Processing helix chain 'D' and resid 719 through 739 removed outlier: 3.771A pdb=" N THR D 723 " --> pdb=" O GLY D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 743 through 771 removed outlier: 3.709A pdb=" N ILE D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 787 Processing helix chain 'D' and resid 787 through 799 removed outlier: 4.084A pdb=" N PHE D 791 " --> pdb=" O THR D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 802 No H-bonds generated for 'chain 'D' and resid 800 through 802' Processing helix chain 'D' and resid 808 through 829 removed outlier: 3.897A pdb=" N LEU D 828 " --> pdb=" O ASP D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 846 Processing helix chain 'D' and resid 849 through 859 removed outlier: 3.981A pdb=" N LYS D 859 " --> pdb=" O SER D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 872 Processing helix chain 'D' and resid 875 through 889 removed outlier: 3.614A pdb=" N LYS D 879 " --> pdb=" O GLU D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 915 removed outlier: 3.697A pdb=" N GLN D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 931 removed outlier: 3.739A pdb=" N ARG D 925 " --> pdb=" O ASN D 921 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET D 931 " --> pdb=" O ILE D 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 635 Processing helix chain 'E' and resid 640 through 648 removed outlier: 4.021A pdb=" N THR E 646 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 657 removed outlier: 3.854A pdb=" N GLU E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU E 654 " --> pdb=" O PRO E 650 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE E 657 " --> pdb=" O TYR E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 675 removed outlier: 3.696A pdb=" N GLN E 665 " --> pdb=" O ASN E 661 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR E 672 " --> pdb=" O GLU E 668 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP E 673 " --> pdb=" O ALA E 669 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 674 " --> pdb=" O PHE E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 704 removed outlier: 3.718A pdb=" N LEU E 681 " --> pdb=" O PRO E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 717 Processing helix chain 'E' and resid 719 through 739 removed outlier: 3.753A pdb=" N THR E 723 " --> pdb=" O GLY E 719 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 739 " --> pdb=" O LEU E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 742 No H-bonds generated for 'chain 'E' and resid 740 through 742' Processing helix chain 'E' and resid 743 through 771 removed outlier: 3.655A pdb=" N ILE E 747 " --> pdb=" O SER E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 787 Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.284A pdb=" N PHE E 791 " --> pdb=" O THR E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.722A pdb=" N LYS E 801 " --> pdb=" O LEU E 798 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 828 removed outlier: 4.048A pdb=" N LEU E 828 " --> pdb=" O ASP E 824 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 846 Processing helix chain 'E' and resid 849 through 858 Processing helix chain 'E' and resid 864 through 869 Processing helix chain 'E' and resid 876 through 889 removed outlier: 4.241A pdb=" N ALA E 882 " --> pdb=" O VAL E 878 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 884 " --> pdb=" O ARG E 880 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 889 " --> pdb=" O TYR E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 914 removed outlier: 3.920A pdb=" N TYR E 894 " --> pdb=" O GLN E 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 915 through 917 No H-bonds generated for 'chain 'E' and resid 915 through 917' Processing helix chain 'E' and resid 922 through 931 removed outlier: 4.089A pdb=" N MET E 931 " --> pdb=" O ILE E 927 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 635 Processing helix chain 'F' and resid 640 through 648 removed outlier: 4.061A pdb=" N THR F 646 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 657 removed outlier: 3.557A pdb=" N GLU F 652 " --> pdb=" O LEU F 648 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 657 " --> pdb=" O TYR F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 675 removed outlier: 3.819A pdb=" N GLN F 665 " --> pdb=" O ASN F 661 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR F 672 " --> pdb=" O GLU F 668 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TRP F 673 " --> pdb=" O ALA F 669 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 674 " --> pdb=" O PHE F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 703 removed outlier: 3.704A pdb=" N LEU F 681 " --> pdb=" O PRO F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 717 Processing helix chain 'F' and resid 720 through 739 removed outlier: 3.560A pdb=" N GLN F 739 " --> pdb=" O LEU F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 740 through 742 No H-bonds generated for 'chain 'F' and resid 740 through 742' Processing helix chain 'F' and resid 743 through 771 removed outlier: 3.716A pdb=" N ILE F 747 " --> pdb=" O SER F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 775 through 787 Processing helix chain 'F' and resid 787 through 799 removed outlier: 4.167A pdb=" N PHE F 791 " --> pdb=" O THR F 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 829 removed outlier: 4.006A pdb=" N LEU F 828 " --> pdb=" O ASP F 824 " (cutoff:3.500A) Processing helix chain 'F' and resid 841 through 846 Processing helix chain 'F' and resid 849 through 859 removed outlier: 3.906A pdb=" N LYS F 859 " --> pdb=" O SER F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 872 removed outlier: 3.529A pdb=" N LYS F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 875 through 890 removed outlier: 3.664A pdb=" N LYS F 879 " --> pdb=" O GLU F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 890 through 915 removed outlier: 3.981A pdb=" N TYR F 894 " --> pdb=" O GLN F 890 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN F 915 " --> pdb=" O GLU F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 921 through 931 removed outlier: 3.763A pdb=" N ARG F 925 " --> pdb=" O ASN F 921 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET F 931 " --> pdb=" O ILE F 927 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA2, first strand: chain 'B' and resid 707 through 708 Processing sheet with id=AA3, first strand: chain 'C' and resid 707 through 708 Processing sheet with id=AA4, first strand: chain 'D' and resid 707 through 708 Processing sheet with id=AA5, first strand: chain 'E' and resid 707 through 708 Processing sheet with id=AA6, first strand: chain 'F' and resid 707 through 708 1019 hydrogen bonds defined for protein. 3018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2498 1.32 - 1.44: 3809 1.44 - 1.56: 8564 1.56 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 14973 Sorted by residual: bond pdb=" CA SER F 623 " pdb=" CB SER F 623 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.41e-02 5.03e+03 1.63e+01 bond pdb=" N ILE E 927 " pdb=" CA ILE E 927 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.33e-02 5.65e+03 1.26e+01 bond pdb=" C PRO E 650 " pdb=" O PRO E 650 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" CA SER D 623 " pdb=" CB SER D 623 " ideal model delta sigma weight residual 1.530 1.477 0.054 1.75e-02 3.27e+03 9.43e+00 bond pdb=" N VAL E 878 " pdb=" CA VAL E 878 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.38e-02 5.25e+03 8.85e+00 ... (remaining 14968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19829 1.96 - 3.92: 360 3.92 - 5.88: 56 5.88 - 7.83: 6 7.83 - 9.79: 5 Bond angle restraints: 20256 Sorted by residual: angle pdb=" N SER F 623 " pdb=" CA SER F 623 " pdb=" C SER F 623 " ideal model delta sigma weight residual 114.12 106.38 7.74 1.39e+00 5.18e-01 3.10e+01 angle pdb=" N GLN E 871 " pdb=" CA GLN E 871 " pdb=" C GLN E 871 " ideal model delta sigma weight residual 113.72 107.05 6.67 1.30e+00 5.92e-01 2.64e+01 angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.88 106.54 5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" N ASP C 824 " pdb=" CA ASP C 824 " pdb=" C ASP C 824 " ideal model delta sigma weight residual 113.97 107.61 6.36 1.28e+00 6.10e-01 2.47e+01 angle pdb=" CA PHE E 651 " pdb=" CB PHE E 651 " pdb=" CG PHE E 651 " ideal model delta sigma weight residual 113.80 118.45 -4.65 1.00e+00 1.00e+00 2.16e+01 ... (remaining 20251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7674 17.99 - 35.99: 996 35.99 - 53.98: 329 53.98 - 71.98: 71 71.98 - 89.97: 20 Dihedral angle restraints: 9090 sinusoidal: 3759 harmonic: 5331 Sorted by residual: dihedral pdb=" C ASN E 862 " pdb=" N ASN E 862 " pdb=" CA ASN E 862 " pdb=" CB ASN E 862 " ideal model delta harmonic sigma weight residual -122.60 -132.60 10.00 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CG ARG F 930 " pdb=" CD ARG F 930 " pdb=" NE ARG F 930 " pdb=" CZ ARG F 930 " ideal model delta sinusoidal sigma weight residual -90.00 -38.13 -51.87 2 1.50e+01 4.44e-03 1.32e+01 dihedral pdb=" CB GLU A 841 " pdb=" CG GLU A 841 " pdb=" CD GLU A 841 " pdb=" OE1 GLU A 841 " ideal model delta sinusoidal sigma weight residual 0.00 88.96 -88.96 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1828 0.047 - 0.094: 394 0.094 - 0.141: 76 0.141 - 0.188: 13 0.188 - 0.235: 2 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA ASN E 862 " pdb=" N ASN E 862 " pdb=" C ASN E 862 " pdb=" CB ASN E 862 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASP F 624 " pdb=" N ASP F 624 " pdb=" C ASP F 624 " pdb=" CB ASP F 624 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA LEU E 648 " pdb=" N LEU E 648 " pdb=" C LEU E 648 " pdb=" CB LEU E 648 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 2310 not shown) Planarity restraints: 2622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 822 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C CYS C 822 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS C 822 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 823 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 858 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C THR F 858 " -0.030 2.00e-02 2.50e+03 pdb=" O THR F 858 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS F 859 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 899 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C VAL C 899 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL C 899 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 900 " 0.010 2.00e-02 2.50e+03 ... (remaining 2619 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2272 2.75 - 3.29: 13734 3.29 - 3.83: 23509 3.83 - 4.36: 26306 4.36 - 4.90: 47533 Nonbonded interactions: 113354 Sorted by model distance: nonbonded pdb=" N GLU C 923 " pdb=" OE1 GLU C 923 " model vdw 2.218 3.120 nonbonded pdb=" OD1 ASP E 824 " pdb=" OG SER E 849 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP D 700 " pdb=" NH2 ARG D 708 " model vdw 2.239 3.120 nonbonded pdb=" O ARG A 863 " pdb=" ND2 ASN A 867 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR B 779 " pdb=" OD2 ASP B 824 " model vdw 2.261 3.040 ... (remaining 113349 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 621 through 933) selection = (chain 'B' and resid 621 through 933) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 621 through 933) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.580 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: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.004 0.057 14973 Z= 0.238 Angle : 0.630 9.792 20256 Z= 0.388 Chirality : 0.042 0.235 2313 Planarity : 0.004 0.046 2622 Dihedral : 18.478 89.971 5616 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.60 % Allowed : 24.25 % Favored : 72.15 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.21), residues: 1803 helix: 2.47 (0.14), residues: 1386 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 930 TYR 0.011 0.001 TYR F 894 PHE 0.022 0.002 PHE E 651 TRP 0.008 0.001 TRP E 673 HIS 0.005 0.001 HIS E 758 Details of bonding type rmsd covalent geometry : bond 0.00435 (14973) covalent geometry : angle 0.63013 (20256) hydrogen bonds : bond 0.14543 ( 1019) hydrogen bonds : angle 4.17250 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 425 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 GLN cc_start: 0.7611 (mp10) cc_final: 0.7340 (mp10) REVERT: B 858 THR cc_start: 0.8434 (t) cc_final: 0.8207 (t) REVERT: C 708 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8612 (ttm170) REVERT: E 764 ASP cc_start: 0.8011 (t0) cc_final: 0.7792 (t0) REVERT: E 817 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8154 (tp) REVERT: E 868 VAL cc_start: 0.6784 (OUTLIER) cc_final: 0.6557 (p) REVERT: E 876 ASP cc_start: 0.5616 (OUTLIER) cc_final: 0.5301 (t70) REVERT: E 880 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5900 (mmt-90) REVERT: E 908 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6965 (ttm170) REVERT: F 847 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8098 (mmtt) outliers start: 59 outliers final: 38 residues processed: 474 average time/residue: 0.6417 time to fit residues: 330.1872 Evaluate side-chains 458 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 415 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 909 MET Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 802 SER Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 679 ASP Chi-restraints excluded: chain E residue 704 ASN Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 748 SER Chi-restraints excluded: chain E residue 759 ARG Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 871 GLN Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 878 VAL Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 880 ARG Chi-restraints excluded: chain F residue 662 ILE Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Chi-restraints excluded: chain F residue 888 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN B 704 ASN B 761 GLN C 742 ASN E 742 ASN E 785 ASN E 864 GLN ** E 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 671 ASN F 725 ASN F 871 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107769 restraints weight = 20759.942| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.69 r_work: 0.3291 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14973 Z= 0.174 Angle : 0.500 7.758 20256 Z= 0.265 Chirality : 0.038 0.133 2313 Planarity : 0.004 0.047 2622 Dihedral : 7.004 70.297 2052 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.96 % Allowed : 22.18 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.21), residues: 1803 helix: 2.63 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -1.61 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 930 TYR 0.012 0.001 TYR F 894 PHE 0.020 0.002 PHE F 732 TRP 0.006 0.001 TRP B 639 HIS 0.005 0.001 HIS C 758 Details of bonding type rmsd covalent geometry : bond 0.00399 (14973) covalent geometry : angle 0.49982 (20256) hydrogen bonds : bond 0.06905 ( 1019) hydrogen bonds : angle 3.37545 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 396 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.7782 (m-30) cc_final: 0.7521 (m-30) REVERT: A 845 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: A 912 ASP cc_start: 0.7867 (t0) cc_final: 0.7646 (t0) REVERT: C 881 PHE cc_start: 0.8038 (t80) cc_final: 0.7826 (t80) REVERT: C 912 ASP cc_start: 0.7670 (m-30) cc_final: 0.7122 (m-30) REVERT: C 915 GLN cc_start: 0.7932 (pp30) cc_final: 0.7698 (pp30) REVERT: E 868 VAL cc_start: 0.6855 (OUTLIER) cc_final: 0.6564 (p) REVERT: E 876 ASP cc_start: 0.6054 (OUTLIER) cc_final: 0.5845 (t70) REVERT: E 908 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7358 (ttm170) REVERT: F 699 ASP cc_start: 0.7792 (t0) cc_final: 0.7524 (m-30) REVERT: F 700 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: F 847 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8235 (mmtt) REVERT: F 871 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: F 913 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7716 (mp) outliers start: 65 outliers final: 29 residues processed: 438 average time/residue: 0.6328 time to fit residues: 301.2785 Evaluate side-chains 422 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 387 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 880 ARG Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Chi-restraints excluded: chain F residue 913 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN B 704 ASN C 728 ASN C 742 ASN E 635 ASN E 742 ASN E 785 ASN E 871 GLN E 926 ASN F 671 ASN F 725 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107913 restraints weight = 20837.198| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.69 r_work: 0.3311 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14973 Z= 0.171 Angle : 0.481 8.026 20256 Z= 0.253 Chirality : 0.038 0.130 2313 Planarity : 0.004 0.045 2622 Dihedral : 5.649 59.358 2006 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.84 % Allowed : 21.69 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.20), residues: 1803 helix: 2.69 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -1.73 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 930 TYR 0.013 0.002 TYR F 894 PHE 0.021 0.002 PHE D 732 TRP 0.006 0.001 TRP B 639 HIS 0.005 0.001 HIS C 758 Details of bonding type rmsd covalent geometry : bond 0.00400 (14973) covalent geometry : angle 0.48060 (20256) hydrogen bonds : bond 0.06714 ( 1019) hydrogen bonds : angle 3.24773 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 402 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.7790 (m-30) cc_final: 0.7540 (m-30) REVERT: A 845 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: A 912 ASP cc_start: 0.7821 (t0) cc_final: 0.7599 (t0) REVERT: A 915 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7467 (mp-120) REVERT: C 699 ASP cc_start: 0.7838 (t70) cc_final: 0.7563 (t70) REVERT: C 881 PHE cc_start: 0.8004 (t80) cc_final: 0.7793 (t80) REVERT: C 886 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6637 (mtm) REVERT: C 908 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7361 (ttt90) REVERT: C 911 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7976 (mm-30) REVERT: C 912 ASP cc_start: 0.7672 (m-30) cc_final: 0.7080 (m-30) REVERT: C 913 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (tt) REVERT: C 915 GLN cc_start: 0.7951 (pp30) cc_final: 0.7700 (pp30) REVERT: D 738 VAL cc_start: 0.8523 (t) cc_final: 0.8165 (p) REVERT: D 781 ASP cc_start: 0.8021 (m-30) cc_final: 0.7750 (m-30) REVERT: D 873 SER cc_start: 0.8465 (p) cc_final: 0.8041 (t) REVERT: E 819 PHE cc_start: 0.8083 (m-10) cc_final: 0.7842 (m-10) REVERT: E 868 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6632 (p) REVERT: E 874 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6437 (ptpp) REVERT: E 876 ASP cc_start: 0.6156 (OUTLIER) cc_final: 0.5021 (t70) REVERT: E 880 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6081 (mmt-90) REVERT: E 908 ARG cc_start: 0.7762 (ttm170) cc_final: 0.7308 (ttm170) REVERT: F 699 ASP cc_start: 0.7784 (t0) cc_final: 0.7507 (m-30) REVERT: F 700 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: F 847 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8230 (mmtt) REVERT: F 871 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: F 913 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7787 (mp) outliers start: 63 outliers final: 30 residues processed: 434 average time/residue: 0.6296 time to fit residues: 297.0009 Evaluate side-chains 427 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 386 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 886 MET Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 880 ARG Chi-restraints excluded: chain E residue 922 ILE Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 790 LEU Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Chi-restraints excluded: chain F residue 913 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 47 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 48 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 704 ASN C 742 ASN C 785 ASN C 903 ASN D 671 ASN E 635 ASN E 742 ASN E 785 ASN E 926 ASN F 725 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108067 restraints weight = 20471.642| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.67 r_work: 0.3304 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14973 Z= 0.195 Angle : 0.499 8.294 20256 Z= 0.261 Chirality : 0.039 0.132 2313 Planarity : 0.004 0.038 2622 Dihedral : 5.336 59.731 1999 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.51 % Allowed : 20.96 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.20), residues: 1803 helix: 2.68 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -1.86 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 930 TYR 0.013 0.002 TYR F 894 PHE 0.023 0.002 PHE D 732 TRP 0.007 0.001 TRP E 673 HIS 0.005 0.001 HIS C 758 Details of bonding type rmsd covalent geometry : bond 0.00468 (14973) covalent geometry : angle 0.49876 (20256) hydrogen bonds : bond 0.07189 ( 1019) hydrogen bonds : angle 3.27727 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 405 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.7827 (m-30) cc_final: 0.7610 (m-30) REVERT: A 782 MET cc_start: 0.8480 (tmm) cc_final: 0.8231 (tmm) REVERT: A 827 ASN cc_start: 0.8576 (t0) cc_final: 0.8373 (t160) REVERT: A 845 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: A 912 ASP cc_start: 0.7862 (t0) cc_final: 0.7660 (t0) REVERT: A 915 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7386 (mp-120) REVERT: B 823 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: C 699 ASP cc_start: 0.7860 (t70) cc_final: 0.7590 (t70) REVERT: C 881 PHE cc_start: 0.7976 (t80) cc_final: 0.7775 (t80) REVERT: C 886 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6595 (mtm) REVERT: C 908 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7350 (ttt90) REVERT: C 912 ASP cc_start: 0.7731 (m-30) cc_final: 0.7089 (m-30) REVERT: C 915 GLN cc_start: 0.7972 (pp30) cc_final: 0.7733 (pp30) REVERT: D 738 VAL cc_start: 0.8561 (t) cc_final: 0.8191 (p) REVERT: D 823 ASP cc_start: 0.7923 (t0) cc_final: 0.7708 (t0) REVERT: D 873 SER cc_start: 0.8468 (p) cc_final: 0.8052 (t) REVERT: E 874 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6518 (ptpp) REVERT: E 876 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5140 (t70) REVERT: E 880 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6308 (mmt-90) REVERT: E 923 GLU cc_start: 0.7721 (mp0) cc_final: 0.7058 (mp0) REVERT: F 699 ASP cc_start: 0.7767 (t0) cc_final: 0.7488 (m-30) REVERT: F 700 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: F 847 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8181 (mmtt) REVERT: F 871 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: F 913 LEU cc_start: 0.8099 (mt) cc_final: 0.7811 (mp) outliers start: 74 outliers final: 38 residues processed: 439 average time/residue: 0.6340 time to fit residues: 302.5543 Evaluate side-chains 444 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 397 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 886 MET Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 725 ASN Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 880 ARG Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 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 867 ASN B 704 ASN C 742 ASN C 785 ASN E 635 ASN E 742 ASN E 785 ASN E 926 ASN F 725 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108922 restraints weight = 20537.872| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.68 r_work: 0.3328 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14973 Z= 0.159 Angle : 0.470 8.416 20256 Z= 0.247 Chirality : 0.038 0.131 2313 Planarity : 0.004 0.039 2622 Dihedral : 5.212 58.514 1998 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.84 % Allowed : 21.94 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.20), residues: 1803 helix: 2.81 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -1.81 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 930 TYR 0.011 0.001 TYR F 894 PHE 0.020 0.002 PHE F 732 TRP 0.006 0.001 TRP B 639 HIS 0.004 0.001 HIS D 758 Details of bonding type rmsd covalent geometry : bond 0.00367 (14973) covalent geometry : angle 0.46979 (20256) hydrogen bonds : bond 0.06447 ( 1019) hydrogen bonds : angle 3.17261 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 385 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 ASN cc_start: 0.8552 (t0) cc_final: 0.8323 (t0) REVERT: A 700 ASP cc_start: 0.7761 (m-30) cc_final: 0.7555 (m-30) REVERT: A 782 MET cc_start: 0.8467 (tmm) cc_final: 0.8220 (tmm) REVERT: A 827 ASN cc_start: 0.8524 (t0) cc_final: 0.8308 (t160) REVERT: A 845 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: A 911 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 915 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7387 (mp-120) REVERT: C 699 ASP cc_start: 0.7824 (t70) cc_final: 0.7542 (t70) REVERT: C 881 PHE cc_start: 0.7957 (t80) cc_final: 0.7743 (t80) REVERT: C 886 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6574 (mtm) REVERT: C 908 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7348 (ttt90) REVERT: C 911 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7926 (mm-30) REVERT: C 912 ASP cc_start: 0.7703 (m-30) cc_final: 0.7074 (m-30) REVERT: C 915 GLN cc_start: 0.7985 (pp30) cc_final: 0.7753 (pp30) REVERT: D 738 VAL cc_start: 0.8498 (t) cc_final: 0.8131 (p) REVERT: D 873 SER cc_start: 0.8437 (p) cc_final: 0.8033 (t) REVERT: E 817 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8172 (tp) REVERT: E 876 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.6051 (t70) REVERT: E 923 GLU cc_start: 0.7745 (mp0) cc_final: 0.7056 (mp0) REVERT: F 699 ASP cc_start: 0.7752 (t0) cc_final: 0.7470 (m-30) REVERT: F 700 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: F 847 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8178 (mmtt) REVERT: F 871 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7397 (mp10) outliers start: 63 outliers final: 35 residues processed: 418 average time/residue: 0.6210 time to fit residues: 282.3149 Evaluate side-chains 419 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 886 MET Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 725 ASN Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 790 LEU Chi-restraints excluded: chain F residue 800 ILE Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 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 867 ASN B 704 ASN C 742 ASN C 785 ASN E 742 ASN E 785 ASN F 725 ASN F 916 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109460 restraints weight = 20393.723| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.67 r_work: 0.3327 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14973 Z= 0.158 Angle : 0.470 9.058 20256 Z= 0.246 Chirality : 0.038 0.131 2313 Planarity : 0.004 0.039 2622 Dihedral : 4.882 57.999 1990 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.72 % Allowed : 22.55 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.20), residues: 1803 helix: 2.90 (0.14), residues: 1413 sheet: None (None), residues: 0 loop : -1.90 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 930 TYR 0.011 0.001 TYR F 894 PHE 0.020 0.002 PHE F 732 TRP 0.006 0.001 TRP B 639 HIS 0.005 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00367 (14973) covalent geometry : angle 0.46978 (20256) hydrogen bonds : bond 0.06346 ( 1019) hydrogen bonds : angle 3.14114 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 390 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 ASN cc_start: 0.8552 (t0) cc_final: 0.8326 (t0) REVERT: A 845 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: A 915 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7392 (mp-120) REVERT: C 699 ASP cc_start: 0.7825 (t70) cc_final: 0.7567 (t70) REVERT: C 881 PHE cc_start: 0.7952 (t80) cc_final: 0.7741 (t80) REVERT: C 886 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6573 (mtm) REVERT: C 908 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7341 (ttt180) REVERT: C 911 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7909 (mm-30) REVERT: C 912 ASP cc_start: 0.7675 (m-30) cc_final: 0.7021 (m-30) REVERT: C 915 GLN cc_start: 0.7992 (pp30) cc_final: 0.7740 (pp30) REVERT: D 738 VAL cc_start: 0.8501 (t) cc_final: 0.8144 (p) REVERT: D 873 SER cc_start: 0.8410 (p) cc_final: 0.8012 (t) REVERT: E 817 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8176 (tp) REVERT: E 876 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6176 (t70) REVERT: F 699 ASP cc_start: 0.7744 (t0) cc_final: 0.7463 (m-30) REVERT: F 700 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: F 847 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8161 (mmtt) REVERT: F 871 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7417 (mp10) outliers start: 61 outliers final: 37 residues processed: 421 average time/residue: 0.6214 time to fit residues: 284.5467 Evaluate side-chains 424 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 380 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 886 MET Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 725 ASN Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.0980 chunk 149 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 155 optimal weight: 0.0060 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 742 ASN C 785 ASN E 635 ASN E 725 ASN E 742 ASN E 785 ASN E 921 ASN F 725 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110819 restraints weight = 20322.600| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.62 r_work: 0.3373 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14973 Z= 0.124 Angle : 0.443 8.545 20256 Z= 0.233 Chirality : 0.036 0.128 2313 Planarity : 0.003 0.038 2622 Dihedral : 4.760 56.580 1990 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.74 % Allowed : 23.95 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.20), residues: 1803 helix: 3.04 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -1.78 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 930 TYR 0.022 0.001 TYR E 885 PHE 0.017 0.001 PHE F 732 TRP 0.005 0.001 TRP B 639 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00266 (14973) covalent geometry : angle 0.44340 (20256) hydrogen bonds : bond 0.05337 ( 1019) hydrogen bonds : angle 3.00917 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7341 (mp-120) REVERT: C 881 PHE cc_start: 0.7947 (t80) cc_final: 0.7740 (t80) REVERT: C 886 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6539 (mtm) REVERT: C 908 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7336 (ttt180) REVERT: C 912 ASP cc_start: 0.7661 (m-30) cc_final: 0.7027 (m-30) REVERT: C 915 GLN cc_start: 0.8007 (pp30) cc_final: 0.7773 (pp30) REVERT: D 642 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6681 (t0) REVERT: D 704 ASN cc_start: 0.8288 (t0) cc_final: 0.8048 (t160) REVERT: D 738 VAL cc_start: 0.8445 (t) cc_final: 0.8090 (p) REVERT: D 781 ASP cc_start: 0.8011 (m-30) cc_final: 0.7781 (m-30) REVERT: D 873 SER cc_start: 0.8369 (p) cc_final: 0.7989 (t) REVERT: E 817 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8157 (tp) REVERT: E 876 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6215 (t70) REVERT: E 886 MET cc_start: 0.5299 (ttp) cc_final: 0.4468 (ttm) REVERT: E 923 GLU cc_start: 0.7771 (mp0) cc_final: 0.7393 (mp0) REVERT: F 699 ASP cc_start: 0.7658 (t0) cc_final: 0.7394 (m-30) REVERT: F 700 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: F 847 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8136 (mmtt) REVERT: F 871 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7362 (mp10) outliers start: 45 outliers final: 28 residues processed: 401 average time/residue: 0.6298 time to fit residues: 274.2266 Evaluate side-chains 400 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 365 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 886 MET Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 817 ILE Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain E residue 922 ILE Chi-restraints excluded: chain F residue 662 ILE Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 178 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 742 ASN C 785 ASN E 635 ASN E 742 ASN E 785 ASN F 725 ASN F 916 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104770 restraints weight = 20473.205| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.64 r_work: 0.3286 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14973 Z= 0.243 Angle : 0.541 9.338 20256 Z= 0.281 Chirality : 0.042 0.136 2313 Planarity : 0.004 0.038 2622 Dihedral : 4.931 59.815 1990 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.53 % Allowed : 23.46 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.20), residues: 1803 helix: 2.71 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 930 TYR 0.016 0.002 TYR B 825 PHE 0.027 0.002 PHE D 732 TRP 0.010 0.002 TRP C 767 HIS 0.006 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00598 (14973) covalent geometry : angle 0.54114 (20256) hydrogen bonds : bond 0.07878 ( 1019) hydrogen bonds : angle 3.33844 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 439 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7402 (mp-120) REVERT: C 829 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7727 (mtmm) REVERT: C 881 PHE cc_start: 0.7973 (t80) cc_final: 0.7760 (t80) REVERT: C 911 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7984 (mm-30) REVERT: C 912 ASP cc_start: 0.7745 (m-30) cc_final: 0.7058 (m-30) REVERT: C 915 GLN cc_start: 0.7976 (pp30) cc_final: 0.7724 (pp30) REVERT: C 930 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7624 (ttp80) REVERT: D 709 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8226 (mtt180) REVERT: D 782 MET cc_start: 0.8202 (tmt) cc_final: 0.7876 (tmt) REVERT: D 847 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8151 (mmtt) REVERT: D 873 SER cc_start: 0.8463 (p) cc_final: 0.8048 (t) REVERT: E 876 ASP cc_start: 0.6537 (OUTLIER) cc_final: 0.6297 (t70) REVERT: E 886 MET cc_start: 0.5370 (ttp) cc_final: 0.4624 (ttm) REVERT: E 923 GLU cc_start: 0.7844 (mp0) cc_final: 0.7466 (mp0) REVERT: F 699 ASP cc_start: 0.7811 (t0) cc_final: 0.7540 (m-30) REVERT: F 847 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8140 (mmtt) REVERT: F 871 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7443 (mp10) outliers start: 58 outliers final: 34 residues processed: 463 average time/residue: 0.6759 time to fit residues: 339.4936 Evaluate side-chains 466 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 428 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 803 THR Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 93 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 165 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 704 ASN B 862 ASN C 742 ASN C 785 ASN D 871 GLN E 635 ASN E 671 ASN E 742 ASN E 785 ASN F 725 ASN F 916 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108029 restraints weight = 20460.552| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.64 r_work: 0.3343 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14973 Z= 0.149 Angle : 0.482 9.134 20256 Z= 0.254 Chirality : 0.037 0.129 2313 Planarity : 0.004 0.038 2622 Dihedral : 4.800 57.065 1988 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.50 % Allowed : 24.86 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.20), residues: 1803 helix: 2.93 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -1.85 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 930 TYR 0.018 0.001 TYR E 885 PHE 0.018 0.001 PHE F 732 TRP 0.006 0.001 TRP B 639 HIS 0.004 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00337 (14973) covalent geometry : angle 0.48204 (20256) hydrogen bonds : bond 0.06149 ( 1019) hydrogen bonds : angle 3.14766 ( 3018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 369 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7387 (mp-120) REVERT: C 824 ASP cc_start: 0.7701 (t0) cc_final: 0.7441 (t0) REVERT: C 829 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7710 (mtmm) REVERT: C 881 PHE cc_start: 0.7943 (t80) cc_final: 0.7729 (t80) REVERT: C 908 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7346 (ttt180) REVERT: C 912 ASP cc_start: 0.7752 (m-30) cc_final: 0.7066 (m-30) REVERT: C 915 GLN cc_start: 0.7968 (pp30) cc_final: 0.7723 (pp30) REVERT: C 930 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7585 (ttp80) REVERT: D 709 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8191 (mtt180) REVERT: D 738 VAL cc_start: 0.8492 (t) cc_final: 0.8131 (p) REVERT: D 782 MET cc_start: 0.8101 (tmt) cc_final: 0.7817 (tmt) REVERT: D 873 SER cc_start: 0.8382 (p) cc_final: 0.8007 (t) REVERT: E 876 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6300 (t70) REVERT: E 886 MET cc_start: 0.5410 (ttp) cc_final: 0.4727 (ttm) REVERT: F 699 ASP cc_start: 0.7765 (t0) cc_final: 0.7474 (m-30) REVERT: F 847 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8130 (mmtt) REVERT: F 871 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: F 913 LEU cc_start: 0.8063 (mt) cc_final: 0.7769 (mp) outliers start: 41 outliers final: 30 residues processed: 394 average time/residue: 0.7058 time to fit residues: 301.4423 Evaluate side-chains 399 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 365 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 790 LEU Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 128 optimal weight: 0.0670 chunk 167 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 635 ASN E 742 ASN E 785 ASN F 725 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109448 restraints weight = 20236.787| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.60 r_work: 0.3356 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14973 Z= 0.144 Angle : 0.482 9.387 20256 Z= 0.253 Chirality : 0.037 0.131 2313 Planarity : 0.004 0.041 2622 Dihedral : 4.731 56.640 1988 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.13 % Allowed : 25.59 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.20), residues: 1803 helix: 3.01 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 930 TYR 0.017 0.001 TYR E 885 PHE 0.019 0.002 PHE F 732 TRP 0.006 0.001 TRP B 639 HIS 0.004 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00325 (14973) covalent geometry : angle 0.48172 (20256) hydrogen bonds : bond 0.05913 ( 1019) hydrogen bonds : angle 3.11111 ( 3018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 360 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 782 MET cc_start: 0.8537 (tmm) cc_final: 0.8322 (tmm) REVERT: A 915 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7363 (mp-120) REVERT: C 824 ASP cc_start: 0.7664 (t0) cc_final: 0.7440 (t0) REVERT: C 829 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7695 (mtmm) REVERT: C 881 PHE cc_start: 0.7947 (t80) cc_final: 0.7739 (t80) REVERT: C 908 ARG cc_start: 0.7918 (ttm170) cc_final: 0.7507 (ttt180) REVERT: C 912 ASP cc_start: 0.7689 (m-30) cc_final: 0.7057 (m-30) REVERT: C 915 GLN cc_start: 0.7945 (pp30) cc_final: 0.7698 (pp30) REVERT: D 738 VAL cc_start: 0.8478 (t) cc_final: 0.8117 (p) REVERT: D 782 MET cc_start: 0.8080 (tmt) cc_final: 0.7836 (tmt) REVERT: D 873 SER cc_start: 0.8396 (p) cc_final: 0.8010 (t) REVERT: E 703 ASP cc_start: 0.6810 (m-30) cc_final: 0.6605 (m-30) REVERT: E 876 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.6333 (t70) REVERT: E 886 MET cc_start: 0.5351 (ttp) cc_final: 0.4709 (ttm) REVERT: F 699 ASP cc_start: 0.7745 (t0) cc_final: 0.7475 (m-30) REVERT: F 847 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8134 (mmtt) REVERT: F 871 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: F 913 LEU cc_start: 0.8054 (mt) cc_final: 0.7743 (mp) outliers start: 35 outliers final: 27 residues processed: 385 average time/residue: 0.7165 time to fit residues: 298.8712 Evaluate side-chains 388 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 357 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 879 LYS Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 866 ILE Chi-restraints excluded: chain F residue 871 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 704 ASN E 635 ASN E 742 ASN E 785 ASN F 725 ASN F 916 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108366 restraints weight = 20295.822| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.65 r_work: 0.3326 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14973 Z= 0.179 Angle : 0.510 9.174 20256 Z= 0.266 Chirality : 0.039 0.134 2313 Planarity : 0.004 0.042 2622 Dihedral : 4.623 57.914 1986 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.68 % Allowed : 24.74 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.20), residues: 1803 helix: 2.93 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 930 TYR 0.017 0.002 TYR E 885 PHE 0.022 0.002 PHE D 732 TRP 0.006 0.001 TRP B 639 HIS 0.005 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00425 (14973) covalent geometry : angle 0.51007 (20256) hydrogen bonds : bond 0.06652 ( 1019) hydrogen bonds : angle 3.19995 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7049.19 seconds wall clock time: 120 minutes 30.42 seconds (7230.42 seconds total)