Starting phenix.real_space_refine on Sun Sep 13 13:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx3_30894/09_2026/7dx3_30894.map" } resolution = 3.5 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= 0.000 sd= 0.005 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 102 5.16 5 C 15100 2.51 5 N 3858 2.21 5 O 4692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23752 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7590 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 9 Chain: "B" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.98, per 1000 atoms: 0.21 Number of scatterers: 23752 At special positions: 0 Unit cell: (135.875, 154.354, 169.572, 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 102 16.00 O 4692 8.00 N 3858 7.00 C 15100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.23 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.52 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.28 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.73 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.21 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.34 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.96 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.11 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.15 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 343 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 847.9 milliseconds 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5468 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 41 sheets defined 25.1% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.648A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.559A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.606A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.354A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.991A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 removed outlier: 5.268A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.729A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.684A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.399A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.193A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.905A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD8, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.339A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.548A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 888 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5260 1.33 - 1.45: 6107 1.45 - 1.58: 12757 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 24253 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.30e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.81e+01 bond pdb=" CA MET A 697 " pdb=" C MET A 697 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.34e+01 bond pdb=" N SER A 698 " pdb=" CA SER A 698 " ideal model delta sigma weight residual 1.456 1.418 0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" C LEU A 223 " pdb=" N GLU A 224 " ideal model delta sigma weight residual 1.331 1.391 -0.060 2.07e-02 2.33e+03 8.36e+00 ... (remaining 24248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 31992 2.55 - 5.10: 921 5.10 - 7.66: 59 7.66 - 10.21: 13 10.21 - 12.76: 4 Bond angle restraints: 32989 Sorted by residual: angle pdb=" N GLN B 314 " pdb=" CA GLN B 314 " pdb=" C GLN B 314 " ideal model delta sigma weight residual 110.50 97.74 12.76 1.41e+00 5.03e-01 8.19e+01 angle pdb=" N CYS A 538 " pdb=" CA CYS A 538 " pdb=" C CYS A 538 " ideal model delta sigma weight residual 110.10 100.87 9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.42e+01 ... (remaining 32984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11881 17.93 - 35.86: 1391 35.86 - 53.79: 449 53.79 - 71.72: 124 71.72 - 89.65: 43 Dihedral angle restraints: 13888 sinusoidal: 5410 harmonic: 8478 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 13885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 3968 0.329 - 0.658: 4 0.658 - 0.987: 4 0.987 - 1.316: 0 1.316 - 1.644: 1 Chirality restraints: 3977 Sorted by residual: chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.76e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 3974 not shown) Planarity restraints: 4215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.066 2.00e-02 2.50e+03 9.32e-02 1.09e+02 pdb=" CG ASN B 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.164 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.035 2.00e-02 2.50e+03 6.62e-02 5.49e+01 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.119 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.046 2.00e-02 2.50e+03 6.11e-02 4.67e+01 pdb=" CG ASN C 331 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.107 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 4212 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 139 2.44 - 3.06: 15324 3.06 - 3.67: 32793 3.67 - 4.29: 52162 4.29 - 4.90: 86706 Nonbonded interactions: 187124 Sorted by model distance: nonbonded pdb=" O SER B 530 " pdb=" O THR B 531 " model vdw 1.828 3.040 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 3.120 nonbonded pdb=" O SER B 316 " pdb=" ND2 ASN B 317 " model vdw 2.032 3.120 ... (remaining 187119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1408)) selection = (chain 'B' and resid 27 through 1408) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.290 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.013 0.493 24360 Z= 0.583 Angle : 1.388 52.467 33274 Z= 0.712 Chirality : 0.074 1.644 3977 Planarity : 0.007 0.094 4167 Dihedral : 18.350 89.646 8312 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 3.08 % Allowed : 10.58 % Favored : 86.33 % Rotamer: Outliers : 12.74 % Allowed : 17.84 % Favored : 69.42 % 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: -4.13 (0.13), residues: 2854 helix: -2.21 (0.16), residues: 662 sheet: -1.95 (0.18), residues: 710 loop : -3.49 (0.12), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.004 TRP A 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01198 / 0.52 (24253) covalent geometry : angle 1.02375 / 0.59 (32989) SS BOND : bond 0.12960 / 7.68 ( 36) SS BOND : angle 15.57032 / 10.13 ( 72) hydrogen bonds : bond 0.19393 / 12.96 ( 852) hydrogen bonds : angle 7.75403 / 5.19 ( 2403) link_BETA1-4 : bond 0.04102 / 3.08 ( 23) link_BETA1-4 : angle 4.27187 / 2.73 ( 69) link_NAG-ASN : bond 0.02212 / 1.19 ( 48) link_NAG-ASN : angle 8.65152 / 6.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 325 poor density : 442 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.6207 (OUTLIER) cc_final: 0.5992 (t) REVERT: A 153 MET cc_start: -0.2236 (mpp) cc_final: -0.2829 (mtp) REVERT: A 702 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5281 (mm-30) REVERT: A 1132 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8585 (pt) REVERT: B 61 ASN cc_start: 0.3296 (t0) cc_final: 0.2024 (p0) REVERT: B 81 ASN cc_start: 0.6503 (OUTLIER) cc_final: 0.5706 (m-40) REVERT: B 437 ASN cc_start: 0.6470 (t0) cc_final: 0.5806 (p0) REVERT: B 976 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8925 (p) REVERT: C 118 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.5337 (tp) REVERT: C 143 VAL cc_start: 0.4380 (OUTLIER) cc_final: 0.4180 (p) REVERT: C 153 MET cc_start: 0.0328 (mpp) cc_final: -0.2002 (tmm) REVERT: C 194 PHE cc_start: 0.6855 (m-80) cc_final: 0.6485 (m-80) REVERT: C 221 SER cc_start: 0.5562 (OUTLIER) cc_final: 0.5152 (m) REVERT: C 296 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (tp) REVERT: C 540 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7518 (t0) REVERT: C 878 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8931 (mt) outliers start: 325 outliers final: 94 residues processed: 708 average time/residue: 0.1540 time to fit residues: 170.1830 Evaluate side-chains 312 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 207 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 81 ASN A 134 GLN A 137 ASN A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 440 ASN A 498 GLN A 536 ASN A 644 GLN A 762 GLN A 804 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 935 GLN A 955 ASN A 969 ASN A 992 GLN A1125 ASN B 134 GLN B 137 ASN B 207 HIS B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 532 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 655 HIS B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 954 GLN B 992 GLN B1054 GLN C 134 GLN C 137 ASN C 207 HIS C 218 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 498 GLN C 540 ASN C 613 GLN C 644 GLN C 703 ASN C 751 ASN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS C1106 GLN C1125 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094516 restraints weight = 44468.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097094 restraints weight = 23166.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098658 restraints weight = 15671.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099499 restraints weight = 12497.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100136 restraints weight = 11047.863| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24360 Z= 0.221 Angle : 0.869 16.043 33274 Z= 0.424 Chirality : 0.052 0.569 3977 Planarity : 0.006 0.115 4167 Dihedral : 9.063 74.478 3281 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.51 % Favored : 91.10 % Rotamer: Outliers : 6.59 % Allowed : 19.64 % Favored : 73.77 % 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: -2.61 (0.14), residues: 2854 helix: -0.05 (0.20), residues: 652 sheet: -1.18 (0.18), residues: 705 loop : -2.90 (0.13), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 509 TYR 0.023 0.002 TYR B 160 PHE 0.045 0.002 PHE A 329 TRP 0.031 0.002 TRP C 104 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (24253) covalent geometry : angle 0.82959 / 0.41 (32989) SS BOND : bond 0.00554 / 0.31 ( 36) SS BOND : angle 2.81504 / 1.79 ( 72) hydrogen bonds : bond 0.05108 / 3.30 ( 852) hydrogen bonds : angle 5.93276 / 3.99 ( 2403) link_BETA1-4 : bond 0.00663 / 0.35 ( 23) link_BETA1-4 : angle 2.17701 / 1.36 ( 69) link_NAG-ASN : bond 0.00387 / 0.23 ( 48) link_NAG-ASN : angle 3.22790 / 1.98 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 214 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8387 (t) cc_final: 0.8147 (p) REVERT: A 110 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6332 (tp) REVERT: A 118 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7114 (mp) REVERT: A 535 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7585 (mttp) REVERT: B 394 ASN cc_start: 0.5839 (OUTLIER) cc_final: 0.5175 (p0) REVERT: B 437 ASN cc_start: 0.6304 (t0) cc_final: 0.5814 (p0) REVERT: B 530 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.6997 (p) REVERT: B 569 ILE cc_start: 0.6226 (OUTLIER) cc_final: 0.5785 (mt) REVERT: C 90 VAL cc_start: 0.8426 (t) cc_final: 0.7908 (m) REVERT: C 195 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7347 (tptt) REVERT: C 210 ILE cc_start: 0.7588 (tt) cc_final: 0.7098 (mt) REVERT: C 239 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.5525 (mm110) REVERT: C 378 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7739 (mmtm) REVERT: C 529 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7661 (mmmt) REVERT: C 618 THR cc_start: 0.8394 (p) cc_final: 0.7962 (p) REVERT: C 820 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: C 878 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8834 (mt) REVERT: C 1010 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7324 (mp10) outliers start: 168 outliers final: 91 residues processed: 352 average time/residue: 0.1399 time to fit residues: 80.1509 Evaluate side-chains 254 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 151 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 824 ASN B 115 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 913 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092196 restraints weight = 44968.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094769 restraints weight = 23880.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096332 restraints weight = 16281.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097158 restraints weight = 12956.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097812 restraints weight = 11444.896| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24360 Z= 0.218 Angle : 0.787 11.220 33274 Z= 0.379 Chirality : 0.051 0.523 3977 Planarity : 0.005 0.056 4167 Dihedral : 7.103 58.231 3169 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.97 % Favored : 90.82 % Rotamer: Outliers : 5.80 % Allowed : 20.15 % Favored : 74.05 % 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: -2.06 (0.15), residues: 2854 helix: 0.58 (0.21), residues: 651 sheet: -0.88 (0.18), residues: 729 loop : -2.64 (0.14), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.020 0.002 TYR C1067 PHE 0.020 0.002 PHE C 65 TRP 0.027 0.001 TRP C 104 HIS 0.031 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (24253) covalent geometry : angle 0.75098 / 0.37 (32989) SS BOND : bond 0.00523 / 0.31 ( 36) SS BOND : angle 2.49646 / 1.57 ( 72) hydrogen bonds : bond 0.04942 / 3.20 ( 852) hydrogen bonds : angle 5.64730 / 3.79 ( 2403) link_BETA1-4 : bond 0.00551 / 0.30 ( 23) link_BETA1-4 : angle 2.06885 / 1.27 ( 69) link_NAG-ASN : bond 0.00449 / 0.30 ( 48) link_NAG-ASN : angle 2.97811 / 1.85 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 174 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7995 (tt) cc_final: 0.7203 (mp) REVERT: A 317 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7997 (m-40) REVERT: A 565 PHE cc_start: 0.7429 (p90) cc_final: 0.6797 (p90) REVERT: A 1106 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: B 228 ASP cc_start: 0.6379 (t0) cc_final: 0.6157 (t0) REVERT: B 229 LEU cc_start: 0.7672 (mp) cc_final: 0.7154 (tp) REVERT: B 437 ASN cc_start: 0.6270 (t0) cc_final: 0.5780 (p0) REVERT: C 90 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.7858 (m) REVERT: C 195 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7469 (tptt) REVERT: C 227 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7763 (t) REVERT: C 324 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7265 (pp20) REVERT: C 378 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7595 (mmtm) REVERT: C 982 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7762 (t) REVERT: C 1010 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7411 (mp10) outliers start: 148 outliers final: 89 residues processed: 294 average time/residue: 0.1322 time to fit residues: 65.2837 Evaluate side-chains 247 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 150 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 168 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 216 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 121 ASN B 207 HIS B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097119 restraints weight = 44493.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099262 restraints weight = 25567.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099593 restraints weight = 16784.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099889 restraints weight = 16471.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099912 restraints weight = 15331.930| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24360 Z= 0.118 Angle : 0.694 11.114 33274 Z= 0.329 Chirality : 0.048 0.426 3977 Planarity : 0.004 0.056 4167 Dihedral : 6.365 57.701 3149 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.73 % Favored : 93.10 % Rotamer: Outliers : 4.23 % Allowed : 21.83 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.58 (0.15), residues: 2854 helix: 0.99 (0.21), residues: 651 sheet: -0.52 (0.19), residues: 720 loop : -2.36 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 328 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.001 PHE A 135 TRP 0.029 0.001 TRP C 104 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (24253) covalent geometry : angle 0.66280 / 0.32 (32989) SS BOND : bond 0.00391 / 0.25 ( 36) SS BOND : angle 1.81852 / 1.17 ( 72) hydrogen bonds : bond 0.03784 / 2.44 ( 852) hydrogen bonds : angle 5.29404 / 3.56 ( 2403) link_BETA1-4 : bond 0.00625 / 0.33 ( 23) link_BETA1-4 : angle 2.05476 / 1.27 ( 69) link_NAG-ASN : bond 0.00371 / 0.24 ( 48) link_NAG-ASN : angle 2.62783 / 1.61 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 163 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8139 (tt) cc_final: 0.7511 (mp) REVERT: A 135 PHE cc_start: 0.7150 (m-80) cc_final: 0.6934 (m-80) REVERT: A 328 ARG cc_start: 0.5971 (ttm-80) cc_final: 0.5718 (ttm-80) REVERT: A 565 PHE cc_start: 0.7312 (p90) cc_final: 0.6702 (p90) REVERT: B 138 ASP cc_start: 0.3692 (OUTLIER) cc_final: 0.3239 (p0) REVERT: B 228 ASP cc_start: 0.6536 (t0) cc_final: 0.6265 (t0) REVERT: B 229 LEU cc_start: 0.7770 (mp) cc_final: 0.7205 (tp) REVERT: B 386 LYS cc_start: 0.8299 (mppt) cc_final: 0.7928 (mtpp) REVERT: B 437 ASN cc_start: 0.6381 (t0) cc_final: 0.5904 (p0) REVERT: C 102 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.6613 (mmm-85) REVERT: C 117 LEU cc_start: 0.7754 (tp) cc_final: 0.7372 (mt) REVERT: C 195 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7473 (tptt) REVERT: C 324 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7185 (pp20) REVERT: C 378 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7532 (mmtm) REVERT: C 421 TYR cc_start: 0.6734 (p90) cc_final: 0.5402 (m-10) REVERT: C 902 MET cc_start: 0.8852 (tpp) cc_final: 0.8587 (tpt) REVERT: C 1010 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7302 (mp10) outliers start: 108 outliers final: 67 residues processed: 255 average time/residue: 0.1368 time to fit residues: 58.4738 Evaluate side-chains 215 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 144 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 133 optimal weight: 30.0000 chunk 271 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A1011 GLN B 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 913 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.142629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092743 restraints weight = 44520.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094923 restraints weight = 27561.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095284 restraints weight = 18797.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095355 restraints weight = 17322.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095484 restraints weight = 17263.827| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24360 Z= 0.258 Angle : 0.790 18.002 33274 Z= 0.376 Chirality : 0.052 0.765 3977 Planarity : 0.005 0.057 4167 Dihedral : 6.109 56.922 3133 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.48 % Favored : 91.38 % Rotamer: Outliers : 4.94 % Allowed : 21.80 % Favored : 73.27 % 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: -1.67 (0.15), residues: 2854 helix: 0.92 (0.21), residues: 659 sheet: -0.66 (0.18), residues: 732 loop : -2.40 (0.14), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.020 0.002 TYR A1067 PHE 0.022 0.002 PHE A 86 TRP 0.028 0.002 TRP C 104 HIS 0.015 0.002 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (24253) covalent geometry : angle 0.74648 / 0.36 (32989) SS BOND : bond 0.00487 / 0.30 ( 36) SS BOND : angle 2.28411 / 1.37 ( 72) hydrogen bonds : bond 0.04892 / 3.15 ( 852) hydrogen bonds : angle 5.47037 / 3.68 ( 2403) link_BETA1-4 : bond 0.00597 / 0.30 ( 23) link_BETA1-4 : angle 2.12033 / 1.29 ( 69) link_NAG-ASN : bond 0.00418 / 0.23 ( 48) link_NAG-ASN : angle 3.45615 / 2.01 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 149 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7580 (mp) REVERT: A 317 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7943 (m-40) REVERT: A 565 PHE cc_start: 0.7441 (p90) cc_final: 0.6913 (p90) REVERT: A 808 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: A 957 GLN cc_start: 0.8210 (tp-100) cc_final: 0.8007 (tm-30) REVERT: A 979 ASP cc_start: 0.8129 (m-30) cc_final: 0.7895 (m-30) REVERT: A 995 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7662 (mtt180) REVERT: B 138 ASP cc_start: 0.3362 (OUTLIER) cc_final: 0.2879 (p0) REVERT: B 437 ASN cc_start: 0.6357 (t0) cc_final: 0.6006 (p0) REVERT: C 90 VAL cc_start: 0.8407 (t) cc_final: 0.8013 (m) REVERT: C 117 LEU cc_start: 0.7626 (tp) cc_final: 0.7254 (mt) REVERT: C 195 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7617 (tptt) REVERT: C 210 ILE cc_start: 0.7611 (tt) cc_final: 0.7222 (mt) REVERT: C 324 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: C 378 LYS cc_start: 0.7785 (mmtm) cc_final: 0.7435 (mmtm) REVERT: C 878 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8996 (tt) REVERT: C 902 MET cc_start: 0.8932 (tpp) cc_final: 0.8617 (tpt) outliers start: 126 outliers final: 95 residues processed: 256 average time/residue: 0.1349 time to fit residues: 57.6145 Evaluate side-chains 238 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 135 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 16 optimal weight: 0.3980 chunk 278 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 121 ASN B 913 GLN C 115 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.145300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093979 restraints weight = 44459.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096572 restraints weight = 23046.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098164 restraints weight = 15507.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099115 restraints weight = 12277.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099572 restraints weight = 10724.102| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24360 Z= 0.124 Angle : 0.691 17.245 33274 Z= 0.325 Chirality : 0.048 0.573 3977 Planarity : 0.004 0.054 4167 Dihedral : 5.724 56.607 3131 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 4.04 % Allowed : 22.50 % Favored : 73.46 % 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: -1.29 (0.15), residues: 2854 helix: 1.29 (0.21), residues: 644 sheet: -0.36 (0.19), residues: 712 loop : -2.18 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 102 TYR 0.019 0.001 TYR A1067 PHE 0.030 0.001 PHE A 135 TRP 0.025 0.001 TRP C 104 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24253) covalent geometry : angle 0.65291 / 0.32 (32989) SS BOND : bond 0.00460 / 0.30 ( 36) SS BOND : angle 1.72550 / 1.01 ( 72) hydrogen bonds : bond 0.03807 / 2.45 ( 852) hydrogen bonds : angle 5.19942 / 3.50 ( 2403) link_BETA1-4 : bond 0.00591 / 0.32 ( 23) link_BETA1-4 : angle 1.90975 / 1.18 ( 69) link_NAG-ASN : bond 0.00378 / 0.23 ( 48) link_NAG-ASN : angle 3.07323 / 1.73 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 152 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 315 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8701 (p) REVERT: A 317 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7914 (m-40) REVERT: A 565 PHE cc_start: 0.7375 (p90) cc_final: 0.6912 (p90) REVERT: A 957 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7726 (tp-100) REVERT: A 1113 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: B 138 ASP cc_start: 0.3389 (OUTLIER) cc_final: 0.2801 (p0) REVERT: B 340 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.6036 (tm-30) REVERT: B 786 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7892 (mptt) REVERT: C 90 VAL cc_start: 0.8039 (t) cc_final: 0.7609 (m) REVERT: C 117 LEU cc_start: 0.7494 (tp) cc_final: 0.7215 (mt) REVERT: C 195 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7646 (tptt) REVERT: C 210 ILE cc_start: 0.7267 (tt) cc_final: 0.6875 (mt) REVERT: C 239 GLN cc_start: 0.7313 (mm-40) cc_final: 0.5186 (tp40) REVERT: C 378 LYS cc_start: 0.7835 (mmtm) cc_final: 0.7451 (mmtm) REVERT: C 394 ASN cc_start: 0.6704 (t0) cc_final: 0.6298 (t0) REVERT: C 421 TYR cc_start: 0.6707 (p90) cc_final: 0.5501 (m-10) REVERT: C 878 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8881 (tt) REVERT: C 902 MET cc_start: 0.8944 (tpp) cc_final: 0.8640 (tpt) outliers start: 103 outliers final: 74 residues processed: 241 average time/residue: 0.1293 time to fit residues: 52.2157 Evaluate side-chains 220 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 137 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 154 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 422 ASN A 955 ASN A1101 HIS B 121 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.142916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091660 restraints weight = 44167.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094124 restraints weight = 23196.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095674 restraints weight = 15784.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096571 restraints weight = 12574.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097064 restraints weight = 11047.153| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 24360 Z= 0.210 Angle : 0.736 15.418 33274 Z= 0.348 Chirality : 0.049 0.465 3977 Planarity : 0.004 0.056 4167 Dihedral : 5.718 56.909 3128 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.20 % Favored : 91.66 % Rotamer: Outliers : 4.59 % Allowed : 22.15 % Favored : 73.27 % 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: -1.35 (0.15), residues: 2854 helix: 1.25 (0.22), residues: 643 sheet: -0.35 (0.19), residues: 720 loop : -2.26 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.019 0.002 TYR C1067 PHE 0.029 0.002 PHE A 135 TRP 0.021 0.001 TRP C 104 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (24253) covalent geometry : angle 0.69994 / 0.34 (32989) SS BOND : bond 0.00376 / 0.23 ( 36) SS BOND : angle 1.94299 / 1.14 ( 72) hydrogen bonds : bond 0.04529 / 2.91 ( 852) hydrogen bonds : angle 5.28401 / 3.56 ( 2403) link_BETA1-4 : bond 0.00523 / 0.28 ( 23) link_BETA1-4 : angle 1.98100 / 1.22 ( 69) link_NAG-ASN : bond 0.00373 / 0.20 ( 48) link_NAG-ASN : angle 3.04156 / 1.77 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 142 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7690 (mp) REVERT: A 317 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7972 (m-40) REVERT: A 519 HIS cc_start: 0.0722 (OUTLIER) cc_final: 0.0223 (t70) REVERT: A 565 PHE cc_start: 0.7409 (p90) cc_final: 0.6980 (p90) REVERT: A 808 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: A 937 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8338 (m) REVERT: A 957 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7846 (tp-100) REVERT: A 988 GLU cc_start: 0.7298 (tp30) cc_final: 0.6853 (tp30) REVERT: A 995 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7603 (mtt180) REVERT: A 1113 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: B 138 ASP cc_start: 0.3661 (OUTLIER) cc_final: 0.3073 (p0) REVERT: B 786 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7955 (mptt) REVERT: C 33 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7153 (p) REVERT: C 90 VAL cc_start: 0.8321 (t) cc_final: 0.7881 (m) REVERT: C 117 LEU cc_start: 0.7541 (tp) cc_final: 0.7221 (mt) REVERT: C 210 ILE cc_start: 0.7399 (tt) cc_final: 0.7047 (mt) REVERT: C 378 LYS cc_start: 0.7630 (mmtm) cc_final: 0.7139 (mmtm) REVERT: C 394 ASN cc_start: 0.6680 (t0) cc_final: 0.6202 (t0) REVERT: C 421 TYR cc_start: 0.6747 (p90) cc_final: 0.5594 (m-10) REVERT: C 878 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8947 (tt) REVERT: C 902 MET cc_start: 0.8975 (tpp) cc_final: 0.8527 (tpt) outliers start: 117 outliers final: 89 residues processed: 242 average time/residue: 0.1303 time to fit residues: 53.2693 Evaluate side-chains 233 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 133 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 104 optimal weight: 0.0270 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 334 ASN A 955 ASN A1071 GLN B 49 HIS B 121 ASN C 121 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.145703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096601 restraints weight = 44074.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098587 restraints weight = 25264.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099126 restraints weight = 15965.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099368 restraints weight = 14776.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099487 restraints weight = 14323.490| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24360 Z= 0.112 Angle : 0.678 14.113 33274 Z= 0.318 Chirality : 0.047 0.413 3977 Planarity : 0.004 0.052 4167 Dihedral : 5.386 56.798 3128 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 3.49 % Allowed : 23.36 % Favored : 73.15 % 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: -1.09 (0.15), residues: 2854 helix: 1.55 (0.22), residues: 637 sheet: -0.20 (0.19), residues: 704 loop : -2.09 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.019 0.001 TYR C1067 PHE 0.027 0.001 PHE A 135 TRP 0.022 0.001 TRP C 104 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (24253) covalent geometry : angle 0.64470 / 0.31 (32989) SS BOND : bond 0.00425 / 0.31 ( 36) SS BOND : angle 1.32447 / 0.82 ( 72) hydrogen bonds : bond 0.03612 / 2.32 ( 852) hydrogen bonds : angle 5.03308 / 3.39 ( 2403) link_BETA1-4 : bond 0.00551 / 0.30 ( 23) link_BETA1-4 : angle 1.94733 / 1.19 ( 69) link_NAG-ASN : bond 0.00400 / 0.25 ( 48) link_NAG-ASN : angle 2.85918 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 149 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 128 ILE cc_start: 0.8788 (mp) cc_final: 0.8504 (mm) REVERT: A 189 LEU cc_start: 0.8682 (tt) cc_final: 0.8375 (mt) REVERT: A 317 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7859 (m-40) REVERT: A 519 HIS cc_start: 0.0797 (OUTLIER) cc_final: 0.0379 (t70) REVERT: A 565 PHE cc_start: 0.7327 (p90) cc_final: 0.6884 (p90) REVERT: A 937 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8213 (m) REVERT: A 957 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7714 (tp-100) REVERT: A 988 GLU cc_start: 0.7170 (tp30) cc_final: 0.6777 (tp30) REVERT: A 1113 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: B 138 ASP cc_start: 0.3348 (OUTLIER) cc_final: 0.2791 (p0) REVERT: B 786 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7895 (mptt) REVERT: C 33 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7274 (p) REVERT: C 117 LEU cc_start: 0.7627 (tp) cc_final: 0.7275 (mt) REVERT: C 195 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7477 (tptt) REVERT: C 210 ILE cc_start: 0.7330 (tt) cc_final: 0.7014 (mt) REVERT: C 239 GLN cc_start: 0.7442 (mm-40) cc_final: 0.5383 (tp40) REVERT: C 368 LEU cc_start: 0.8476 (mt) cc_final: 0.8255 (tp) REVERT: C 378 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7304 (mmtm) REVERT: C 394 ASN cc_start: 0.6721 (t0) cc_final: 0.6221 (t0) REVERT: C 421 TYR cc_start: 0.6333 (p90) cc_final: 0.5578 (m-10) REVERT: C 878 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (tt) REVERT: C 902 MET cc_start: 0.8940 (tpp) cc_final: 0.8663 (tpt) outliers start: 89 outliers final: 68 residues processed: 227 average time/residue: 0.1294 time to fit residues: 50.0719 Evaluate side-chains 215 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 9 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 chunk 139 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 955 ASN A 978 ASN C 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093960 restraints weight = 44577.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094542 restraints weight = 29020.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094699 restraints weight = 20391.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094888 restraints weight = 21657.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095083 restraints weight = 19001.696| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 24360 Z= 0.273 Angle : 0.798 14.008 33274 Z= 0.378 Chirality : 0.051 0.432 3977 Planarity : 0.005 0.056 4167 Dihedral : 5.776 58.326 3126 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.18 % Favored : 90.68 % Rotamer: Outliers : 4.27 % Allowed : 22.85 % Favored : 72.87 % 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: -1.43 (0.15), residues: 2854 helix: 1.15 (0.21), residues: 642 sheet: -0.29 (0.19), residues: 694 loop : -2.32 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 454 TYR 0.020 0.002 TYR B 904 PHE 0.030 0.002 PHE A 135 TRP 0.021 0.002 TRP C 104 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.27 (24253) covalent geometry : angle 0.76336 / 0.37 (32989) SS BOND : bond 0.00486 / 0.31 ( 36) SS BOND : angle 1.96937 / 1.20 ( 72) hydrogen bonds : bond 0.05166 / 3.31 ( 852) hydrogen bonds : angle 5.40532 / 3.64 ( 2403) link_BETA1-4 : bond 0.00544 / 0.30 ( 23) link_BETA1-4 : angle 2.07985 / 1.28 ( 69) link_NAG-ASN : bond 0.00431 / 0.22 ( 48) link_NAG-ASN : angle 3.09961 / 1.82 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 140 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7674 (mp) REVERT: A 128 ILE cc_start: 0.8788 (mp) cc_final: 0.8481 (mm) REVERT: A 189 LEU cc_start: 0.8738 (tt) cc_final: 0.8469 (mt) REVERT: A 317 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7959 (m-40) REVERT: A 343 ASN cc_start: 0.4741 (OUTLIER) cc_final: 0.2740 (t0) REVERT: A 519 HIS cc_start: 0.0915 (OUTLIER) cc_final: 0.0381 (t70) REVERT: A 565 PHE cc_start: 0.7578 (p90) cc_final: 0.7189 (p90) REVERT: A 808 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: A 937 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8308 (m) REVERT: A 957 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7883 (tp-100) REVERT: A 988 GLU cc_start: 0.7298 (tp30) cc_final: 0.6922 (tp30) REVERT: A 995 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7667 (mtt180) REVERT: A 1113 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8503 (mt0) REVERT: B 138 ASP cc_start: 0.4071 (OUTLIER) cc_final: 0.3404 (p0) REVERT: B 338 PHE cc_start: 0.7454 (m-80) cc_final: 0.7071 (m-80) REVERT: C 33 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7317 (p) REVERT: C 90 VAL cc_start: 0.8423 (t) cc_final: 0.7950 (m) REVERT: C 117 LEU cc_start: 0.7586 (tp) cc_final: 0.7151 (mt) REVERT: C 210 ILE cc_start: 0.7644 (tt) cc_final: 0.7315 (mt) REVERT: C 378 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7200 (mmtm) REVERT: C 394 ASN cc_start: 0.6700 (t0) cc_final: 0.6179 (t0) REVERT: C 421 TYR cc_start: 0.6733 (p90) cc_final: 0.5560 (m-80) outliers start: 109 outliers final: 86 residues processed: 235 average time/residue: 0.1321 time to fit residues: 52.7130 Evaluate side-chains 228 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 132 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 110 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 201 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 189 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094194 restraints weight = 44607.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096751 restraints weight = 23176.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098332 restraints weight = 15688.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099248 restraints weight = 12448.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099849 restraints weight = 10897.966| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24360 Z= 0.114 Angle : 0.679 12.195 33274 Z= 0.318 Chirality : 0.047 0.402 3977 Planarity : 0.004 0.056 4167 Dihedral : 5.341 58.136 3126 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 3.18 % Allowed : 23.87 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.09 (0.15), residues: 2854 helix: 1.56 (0.22), residues: 633 sheet: -0.20 (0.19), residues: 698 loop : -2.08 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.026 0.001 PHE A 135 TRP 0.019 0.001 TRP C 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24253) covalent geometry : angle 0.65023 / 0.31 (32989) SS BOND : bond 0.00342 / 0.23 ( 36) SS BOND : angle 1.37513 / 0.83 ( 72) hydrogen bonds : bond 0.03692 / 2.37 ( 852) hydrogen bonds : angle 5.04740 / 3.40 ( 2403) link_BETA1-4 : bond 0.00549 / 0.30 ( 23) link_BETA1-4 : angle 1.98789 / 1.22 ( 69) link_NAG-ASN : bond 0.00404 / 0.25 ( 48) link_NAG-ASN : angle 2.60377 / 1.49 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 150 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 317 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7878 (m-40) REVERT: A 343 ASN cc_start: 0.4267 (OUTLIER) cc_final: 0.2560 (t0) REVERT: A 519 HIS cc_start: 0.0701 (OUTLIER) cc_final: 0.0321 (t70) REVERT: A 565 PHE cc_start: 0.7394 (p90) cc_final: 0.7025 (p90) REVERT: A 740 MET cc_start: 0.7696 (tpp) cc_final: 0.7225 (tpp) REVERT: A 957 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7740 (tp-100) REVERT: A 988 GLU cc_start: 0.7104 (tp30) cc_final: 0.6752 (tp30) REVERT: A 1113 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: B 84 LEU cc_start: 0.6808 (mt) cc_final: 0.6509 (mp) REVERT: B 138 ASP cc_start: 0.3580 (OUTLIER) cc_final: 0.2954 (p0) REVERT: B 338 PHE cc_start: 0.7474 (m-80) cc_final: 0.7076 (m-80) REVERT: C 33 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7175 (p) REVERT: C 90 VAL cc_start: 0.8016 (t) cc_final: 0.7511 (m) REVERT: C 117 LEU cc_start: 0.7532 (tp) cc_final: 0.7250 (mt) REVERT: C 195 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7586 (tptt) REVERT: C 210 ILE cc_start: 0.7211 (tt) cc_final: 0.6946 (mt) REVERT: C 378 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7444 (mmtm) REVERT: C 389 ASP cc_start: 0.8494 (t0) cc_final: 0.8274 (t0) REVERT: C 394 ASN cc_start: 0.6844 (t0) cc_final: 0.6389 (t0) REVERT: C 421 TYR cc_start: 0.6470 (p90) cc_final: 0.5620 (m-10) REVERT: C 902 MET cc_start: 0.8918 (tpp) cc_final: 0.8639 (tpt) outliers start: 81 outliers final: 66 residues processed: 221 average time/residue: 0.1263 time to fit residues: 47.7461 Evaluate side-chains 211 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 137 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 155 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095878 restraints weight = 44222.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097078 restraints weight = 30288.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097263 restraints weight = 20127.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097383 restraints weight = 20629.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097572 restraints weight = 18907.684| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24360 Z= 0.144 Angle : 0.691 11.369 33274 Z= 0.324 Chirality : 0.048 0.374 3977 Planarity : 0.004 0.053 4167 Dihedral : 5.287 56.208 3125 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.50 % Favored : 92.36 % Rotamer: Outliers : 3.21 % Allowed : 23.95 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.08 (0.15), residues: 2854 helix: 1.56 (0.21), residues: 632 sheet: -0.15 (0.19), residues: 708 loop : -2.10 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.019 0.001 TYR A1067 PHE 0.027 0.001 PHE A 135 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (24253) covalent geometry : angle 0.66230 / 0.32 (32989) SS BOND : bond 0.00337 / 0.22 ( 36) SS BOND : angle 1.60331 / 1.00 ( 72) hydrogen bonds : bond 0.03912 / 2.51 ( 852) hydrogen bonds : angle 5.03397 / 3.39 ( 2403) link_BETA1-4 : bond 0.00549 / 0.29 ( 23) link_BETA1-4 : angle 1.96311 / 1.20 ( 69) link_NAG-ASN : bond 0.00356 / 0.21 ( 48) link_NAG-ASN : angle 2.61404 / 1.50 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4060.34 seconds wall clock time: 70 minutes 56.72 seconds (4256.72 seconds total)