Starting phenix.real_space_refine on Fri Mar 6 21:02:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx9_30900/03_2026/7dx9_30900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx9_30900/03_2026/7dx9_30900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dx9_30900/03_2026/7dx9_30900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx9_30900/03_2026/7dx9_30900.map" model { file = "/net/cci-nas-00/data/ceres_data/7dx9_30900/03_2026/7dx9_30900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx9_30900/03_2026/7dx9_30900.cif" } resolution = 3.6 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= 0.006 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 166 5.16 5 C 22029 2.51 5 N 5629 2.21 5 O 6796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34620 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "C" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.93, per 1000 atoms: 0.23 Number of scatterers: 34620 At special positions: 0 Unit cell: (140.223, 194.573, 245.662, 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 166 16.00 O 6796 8.00 N 5629 7.00 C 22029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.17 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=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.96 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.12 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.04 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=2.17 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=2.11 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.98 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.17 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=2.12 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.14 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.17 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 A1409 " - " NAG A1410 " " 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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-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 A1074 " " 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 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 C1409 " - " ASN C 709 " " NAG D 901 " - " ASN D 322 " " NAG E 901 " - " ASN E 322 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN D 53 " " NAG c 1 " - " ASN D 90 " " NAG d 1 " - " ASN D 103 " " NAG e 1 " - " ASN D 432 " " NAG f 1 " - " ASN D 546 " " NAG g 1 " - " ASN E 53 " " NAG h 1 " - " ASN E 90 " " NAG i 1 " - " ASN E 103 " " NAG j 1 " - " ASN E 432 " " NAG k 1 " - " ASN E 546 " Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7912 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 50 sheets defined 35.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.738A 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 747 through 754 removed outlier: 3.695A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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: 3.964A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 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: 4.257A 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 746 through 754 removed outlier: 3.717A 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: 3.560A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.222A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.258A 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: 3.623A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A 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: 3.630A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.772A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.791A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.755A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.688A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.527A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.549A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.308A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.637A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.549A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.879A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.578A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 53 removed outlier: 3.790A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 81 removed outlier: 3.755A pdb=" N ASN E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 removed outlier: 3.687A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.550A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 208 removed outlier: 3.566A pdb=" N GLU E 208 " --> pdb=" O GLY E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.596A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 4.308A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.552A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 412 " --> pdb=" O MET E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.750A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.579A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.577A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A 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: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.295A 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: 6.947A 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: 3.855A 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: 7.661A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A 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: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.128A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.254A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, 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: 6.441A 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: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, 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=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, 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: 7.211A 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: 3.776A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.473A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 454 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: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.893A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.912A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, 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: 3.678A 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: 6.295A 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: 6.949A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, 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=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.659A 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: 3.776A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.588A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 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: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.234A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.718A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF4, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU E 351 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1323 hydrogen bonds defined for protein. 3675 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: 7.47 Time building geometry restraints manager: 3.73 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: 7653 1.33 - 1.45: 9046 1.45 - 1.58: 18488 1.58 - 1.70: 0 1.70 - 1.83: 235 Bond restraints: 35422 Sorted by residual: bond pdb=" CA SER C 698 " pdb=" C SER C 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.36e+01 bond pdb=" C HIS A1088 " pdb=" N PHE A1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.82e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.81e+01 bond pdb=" N PRO E 426 " pdb=" CD PRO E 426 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO D 346 " pdb=" CD PRO D 346 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 ... (remaining 35417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 46940 2.65 - 5.30: 1122 5.30 - 7.95: 85 7.95 - 10.60: 10 10.60 - 13.25: 5 Bond angle restraints: 48162 Sorted by residual: angle pdb=" N THR E 362 " pdb=" CA THR E 362 " pdb=" C THR E 362 " ideal model delta sigma weight residual 109.76 119.35 -9.59 1.59e+00 3.96e-01 3.64e+01 angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.34 -9.58 1.59e+00 3.96e-01 3.63e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.83 -11.29 1.91e+00 2.74e-01 3.50e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 ... (remaining 48157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 19344 17.93 - 35.85: 2042 35.85 - 53.78: 626 53.78 - 71.71: 197 71.71 - 89.63: 59 Dihedral angle restraints: 22268 sinusoidal: 9988 harmonic: 12280 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -7.66 -78.34 1 1.00e+01 1.00e-02 7.66e+01 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 21.06 71.94 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 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 22265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5601 0.329 - 0.659: 7 0.659 - 0.988: 6 0.988 - 1.318: 0 1.318 - 1.647: 1 Chirality restraints: 5615 Sorted by residual: chirality pdb=" C1 NAG A1410 " pdb=" O4 NAG A1409 " pdb=" C2 NAG A1410 " pdb=" O5 NAG A1410 " 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 F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 ... (remaining 5612 not shown) Planarity restraints: 6172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 2 " 0.354 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG d 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG d 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG d 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG d 2 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG i 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.286 2.00e-02 2.50e+03 2.40e-01 7.17e+02 pdb=" C7 NAG i 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.406 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " -0.010 2.00e-02 2.50e+03 ... (remaining 6169 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 260 2.51 - 3.11: 24313 3.11 - 3.70: 49831 3.70 - 4.30: 75310 4.30 - 4.90: 124247 Nonbonded interactions: 273961 Sorted by model distance: nonbonded pdb=" O ILE C 332 " pdb=" OG1 THR C 333 " model vdw 1.909 3.040 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" O SER E 105 " pdb=" OG SER E 106 " model vdw 1.932 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.983 3.120 ... (remaining 273956 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 1408) selection = chain 'B' selection = (chain 'C' and (resid 27 through 939 or resid 944 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = 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' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 30.560 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.190 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.012 0.933 35560 Z= 0.548 Angle : 1.305 71.311 48531 Z= 0.675 Chirality : 0.072 1.647 5615 Planarity : 0.010 0.306 6112 Dihedral : 17.092 89.633 14221 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 2.00 % Allowed : 8.34 % Favored : 89.67 % Rotamer: Outliers : 9.34 % Allowed : 14.67 % Favored : 75.99 % 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: -4.47 (0.10), residues: 4151 helix: -3.32 (0.09), residues: 1338 sheet: -2.01 (0.17), residues: 753 loop : -3.09 (0.11), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.027 0.003 TYR A1067 PHE 0.026 0.003 PHE C 898 TRP 0.025 0.002 TRP C 104 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01076 (35422) covalent geometry : angle 0.98597 (48162) SS BOND : bond 0.14993 ( 45) SS BOND : angle 15.62471 ( 90) hydrogen bonds : bond 0.24636 ( 1287) hydrogen bonds : angle 8.32547 ( 3675) link_BETA1-4 : bond 0.03510 ( 33) link_BETA1-4 : angle 4.70434 ( 99) link_NAG-ASN : bond 0.02702 ( 60) link_NAG-ASN : angle 8.04002 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 345 poor density : 767 time to evaluate : 1.135 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: A 101 ILE cc_start: 0.7693 (mm) cc_final: 0.7466 (mm) REVERT: A 324 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: A 902 MET cc_start: 0.9141 (tpt) cc_final: 0.8883 (tpt) REVERT: A 1104 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9125 (m) REVERT: B 153 MET cc_start: -0.1095 (mpp) cc_final: -0.2565 (ptt) REVERT: B 195 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8370 (ptmt) REVERT: B 389 ASP cc_start: 0.4200 (OUTLIER) cc_final: 0.3827 (t0) REVERT: C 153 MET cc_start: -0.1681 (mpp) cc_final: -0.2522 (mtm) REVERT: C 690 GLN cc_start: 0.6093 (OUTLIER) cc_final: 0.4198 (mm110) REVERT: C 787 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8119 (mm110) REVERT: C 984 LEU cc_start: 0.6154 (mt) cc_final: 0.5692 (mp) REVERT: C 1104 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8833 (t) REVERT: D 323 MET cc_start: 0.3116 (mmp) cc_final: 0.2844 (mmp) REVERT: D 513 ILE cc_start: 0.6052 (tp) cc_final: 0.5402 (tp) REVERT: E 90 ASN cc_start: 0.0160 (t0) cc_final: -0.0172 (m-40) REVERT: E 344 CYS cc_start: 0.4697 (OUTLIER) cc_final: 0.1718 (p) REVERT: E 361 CYS cc_start: 0.5668 (OUTLIER) cc_final: 0.2094 (p) REVERT: E 462 MET cc_start: 0.0628 (mtp) cc_final: 0.0243 (mmt) outliers start: 345 outliers final: 81 residues processed: 1038 average time/residue: 0.1974 time to fit residues: 333.1787 Evaluate side-chains 417 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 327 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 LEU 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 325 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 425 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 137 ASN A 188 ASN A 239 GLN A 422 ASN A 440 ASN A 644 GLN A 655 HIS A 690 GLN A 901 GLN A 914 ASN A 919 ASN A 920 GLN A 926 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 134 GLN B 137 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 498 GLN B 644 GLN B 703 ASN B 764 ASN B 901 GLN B 914 ASN B 926 GLN B 935 GLN B 992 GLN B1010 GLN B1071 GLN B1101 HIS C 66 HIS C 137 ASN C 188 ASN C 317 ASN C 498 GLN C 644 GLN C 690 GLN C 787 GLN C 901 GLN C 914 ASN C 919 ASN C 926 GLN C 955 ASN C 969 ASN C1101 HIS D 58 ASN D 239 HIS D 277 ASN D 373 HIS D 394 ASN D 417 HIS D 505 HIS D 586 ASN E 24 GLN E 58 ASN E 96 GLN E 175 GLN E 373 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.180774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.144418 restraints weight = 74550.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.141523 restraints weight = 127276.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137979 restraints weight = 101793.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137230 restraints weight = 106911.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137263 restraints weight = 91611.141| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35560 Z= 0.169 Angle : 0.824 14.850 48531 Z= 0.401 Chirality : 0.051 0.537 5615 Planarity : 0.005 0.063 6112 Dihedral : 9.999 91.720 6605 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.38 % Favored : 93.35 % Rotamer: Outliers : 4.47 % Allowed : 18.38 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.68 (0.12), residues: 4151 helix: -0.98 (0.13), residues: 1356 sheet: -1.26 (0.18), residues: 750 loop : -2.57 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 518 TYR 0.040 0.002 TYR E 243 PHE 0.024 0.002 PHE B 565 TRP 0.024 0.002 TRP E 461 HIS 0.010 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00367 (35422) covalent geometry : angle 0.78486 (48162) SS BOND : bond 0.00414 ( 45) SS BOND : angle 2.65146 ( 90) hydrogen bonds : bond 0.05483 ( 1287) hydrogen bonds : angle 5.48079 ( 3675) link_BETA1-4 : bond 0.00645 ( 33) link_BETA1-4 : angle 2.29423 ( 99) link_NAG-ASN : bond 0.00504 ( 60) link_NAG-ASN : angle 3.45419 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 381 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 ASN cc_start: 0.7072 (p0) cc_final: 0.6703 (m110) REVERT: A 452 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6749 (mt) REVERT: A 775 ASP cc_start: 0.8084 (m-30) cc_final: 0.7748 (m-30) REVERT: A 902 MET cc_start: 0.9018 (tpt) cc_final: 0.8579 (tpt) REVERT: A 985 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7244 (p0) REVERT: B 153 MET cc_start: -0.1324 (mpp) cc_final: -0.2695 (ttp) REVERT: B 389 ASP cc_start: 0.4005 (OUTLIER) cc_final: 0.3760 (t0) REVERT: B 878 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8580 (tt) REVERT: B 882 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8786 (mt) REVERT: C 153 MET cc_start: -0.2271 (mpp) cc_final: -0.3431 (ttm) REVERT: C 452 LEU cc_start: 0.4186 (mp) cc_final: 0.3463 (mt) REVERT: C 675 GLN cc_start: 0.6833 (tm-30) cc_final: 0.6631 (tt0) REVERT: C 708 SER cc_start: 0.8714 (p) cc_final: 0.8375 (t) REVERT: C 826 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 1104 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8948 (t) REVERT: D 462 MET cc_start: 0.5874 (ttp) cc_final: 0.5586 (ttt) REVERT: E 90 ASN cc_start: 0.0366 (t0) cc_final: -0.0108 (m110) REVERT: E 177 ARG cc_start: 0.4071 (ttt-90) cc_final: 0.3749 (ttp80) REVERT: E 190 MET cc_start: -0.0334 (ppp) cc_final: -0.2049 (tpp) REVERT: E 249 MET cc_start: 0.2276 (tpt) cc_final: 0.0443 (mmt) REVERT: E 462 MET cc_start: 0.0496 (mtp) cc_final: 0.0106 (mmt) outliers start: 165 outliers final: 103 residues processed: 523 average time/residue: 0.1770 time to fit residues: 157.8741 Evaluate side-chains 391 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 281 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 112 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 351 optimal weight: 0.0970 chunk 414 optimal weight: 20.0000 chunk 373 optimal weight: 50.0000 chunk 386 optimal weight: 20.0000 chunk 402 optimal weight: 30.0000 chunk 372 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 613 GLN A 690 GLN A 703 ASN A 804 GLN A 935 GLN A1002 GLN A1135 ASN B 121 ASN B 360 ASN B1135 ASN C 207 HIS C 450 ASN C 690 GLN C1005 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 373 HIS D 378 HIS D 417 HIS D 599 ASN E 378 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.174932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140646 restraints weight = 73193.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136029 restraints weight = 120618.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132977 restraints weight = 123601.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132878 restraints weight = 113886.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131903 restraints weight = 86502.992| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 35560 Z= 0.251 Angle : 0.833 14.260 48531 Z= 0.401 Chirality : 0.051 0.508 5615 Planarity : 0.005 0.050 6112 Dihedral : 9.022 72.017 6528 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.70 % Favored : 93.09 % Rotamer: Outliers : 5.52 % Allowed : 18.25 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.00 (0.12), residues: 4151 helix: -0.22 (0.14), residues: 1347 sheet: -0.90 (0.18), residues: 734 loop : -2.29 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 214 TYR 0.030 0.002 TYR C 904 PHE 0.027 0.002 PHE C 133 TRP 0.040 0.002 TRP E 461 HIS 0.009 0.002 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00593 (35422) covalent geometry : angle 0.79765 (48162) SS BOND : bond 0.01054 ( 45) SS BOND : angle 2.33986 ( 90) hydrogen bonds : bond 0.05203 ( 1287) hydrogen bonds : angle 5.27223 ( 3675) link_BETA1-4 : bond 0.00625 ( 33) link_BETA1-4 : angle 2.54335 ( 99) link_NAG-ASN : bond 0.00645 ( 60) link_NAG-ASN : angle 3.27798 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 305 time to evaluate : 0.981 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: A 101 ILE cc_start: 0.7795 (mm) cc_final: 0.7511 (mm) REVERT: A 226 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6966 (tp) REVERT: A 380 TYR cc_start: 0.5888 (m-10) cc_final: 0.5565 (m-10) REVERT: A 423 TYR cc_start: 0.5915 (t80) cc_final: 0.5404 (t80) REVERT: A 440 ASN cc_start: 0.7033 (p0) cc_final: 0.6564 (m110) REVERT: B 153 MET cc_start: -0.0998 (mpp) cc_final: -0.2356 (ttp) REVERT: B 195 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8643 (ptmt) REVERT: B 239 GLN cc_start: 0.7928 (tp40) cc_final: 0.7604 (mm110) REVERT: B 546 LEU cc_start: 0.7464 (mp) cc_final: 0.7019 (pp) REVERT: C 46 SER cc_start: 0.7316 (OUTLIER) cc_final: 0.6963 (t) REVERT: C 153 MET cc_start: -0.2135 (mpp) cc_final: -0.3892 (ttm) REVERT: C 287 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: C 347 PHE cc_start: 0.5035 (m-80) cc_final: 0.4529 (m-80) REVERT: C 675 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6677 (tt0) REVERT: C 820 ASP cc_start: 0.7035 (m-30) cc_final: 0.6764 (m-30) REVERT: D 83 TYR cc_start: 0.2833 (m-80) cc_final: 0.2445 (m-80) REVERT: D 217 TYR cc_start: 0.3623 (OUTLIER) cc_final: 0.3286 (m-80) REVERT: E 90 ASN cc_start: 0.0408 (t0) cc_final: -0.0146 (m110) REVERT: E 177 ARG cc_start: 0.4169 (ttt-90) cc_final: 0.3868 (ttp80) REVERT: E 190 MET cc_start: -0.0162 (ppp) cc_final: -0.1731 (tpp) REVERT: E 455 MET cc_start: 0.2363 (ttp) cc_final: 0.2038 (tmm) REVERT: E 462 MET cc_start: 0.1151 (mtp) cc_final: 0.0509 (mmt) outliers start: 204 outliers final: 122 residues processed: 481 average time/residue: 0.1743 time to fit residues: 144.7049 Evaluate side-chains 373 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 246 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 377 optimal weight: 8.9990 chunk 301 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 346 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 607 GLN A 690 GLN C 211 ASN C 690 GLN C 824 ASN C 957 GLN C1106 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN E 96 GLN E 101 GLN E 277 ASN E 417 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.171553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137363 restraints weight = 73401.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133958 restraints weight = 133771.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131275 restraints weight = 114607.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130806 restraints weight = 118666.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130336 restraints weight = 95751.772| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 35560 Z= 0.266 Angle : 0.845 19.388 48531 Z= 0.402 Chirality : 0.052 0.610 5615 Planarity : 0.005 0.048 6112 Dihedral : 8.749 59.898 6507 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.01 % Favored : 92.85 % Rotamer: Outliers : 5.44 % Allowed : 19.46 % Favored : 75.09 % 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: -1.76 (0.12), residues: 4151 helix: 0.06 (0.14), residues: 1347 sheet: -0.73 (0.18), residues: 754 loop : -2.23 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.031 0.002 TYR D 183 PHE 0.026 0.002 PHE D 452 TRP 0.036 0.002 TRP D 203 HIS 0.011 0.002 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00634 (35422) covalent geometry : angle 0.80626 (48162) SS BOND : bond 0.00638 ( 45) SS BOND : angle 2.49910 ( 90) hydrogen bonds : bond 0.05098 ( 1287) hydrogen bonds : angle 5.30032 ( 3675) link_BETA1-4 : bond 0.00626 ( 33) link_BETA1-4 : angle 2.51289 ( 99) link_NAG-ASN : bond 0.00702 ( 60) link_NAG-ASN : angle 3.49442 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 291 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7973 (mm) cc_final: 0.7697 (mm) REVERT: A 453 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5173 (p90) REVERT: A 902 MET cc_start: 0.8913 (tpt) cc_final: 0.8397 (tpt) REVERT: B 153 MET cc_start: -0.0984 (mpp) cc_final: -0.2303 (ptm) REVERT: C 131 CYS cc_start: 0.3873 (OUTLIER) cc_final: 0.3560 (m) REVERT: C 153 MET cc_start: -0.1958 (mpp) cc_final: -0.3825 (ttm) REVERT: C 202 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8046 (tptm) REVERT: C 347 PHE cc_start: 0.5528 (m-80) cc_final: 0.5152 (m-80) REVERT: C 690 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: D 83 TYR cc_start: 0.2980 (m-80) cc_final: 0.2659 (m-80) REVERT: D 129 THR cc_start: 0.5164 (p) cc_final: 0.4872 (t) REVERT: D 197 GLU cc_start: 0.4937 (OUTLIER) cc_final: 0.4519 (pp20) REVERT: D 270 MET cc_start: 0.3948 (mmm) cc_final: 0.3472 (mmm) REVERT: D 358 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4804 (mt) REVERT: D 383 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6764 (mtp) REVERT: D 385 TYR cc_start: 0.5068 (p90) cc_final: 0.4798 (p90) REVERT: E 23 GLU cc_start: 0.3334 (OUTLIER) cc_final: 0.2697 (tp30) REVERT: E 90 ASN cc_start: 0.0679 (t0) cc_final: -0.0017 (m110) REVERT: E 177 ARG cc_start: 0.4093 (ttt-90) cc_final: 0.3787 (ttp80) REVERT: E 190 MET cc_start: 0.0734 (ppp) cc_final: -0.1738 (ttp) REVERT: E 249 MET cc_start: 0.2294 (tpt) cc_final: 0.0712 (mmt) REVERT: E 455 MET cc_start: 0.2508 (ttp) cc_final: 0.1922 (tmm) REVERT: E 462 MET cc_start: 0.1189 (mtp) cc_final: 0.0486 (mmt) REVERT: E 557 MET cc_start: 0.5232 (ppp) cc_final: 0.4996 (ppp) outliers start: 201 outliers final: 133 residues processed: 468 average time/residue: 0.1717 time to fit residues: 138.7576 Evaluate side-chains 382 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 242 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 315 optimal weight: 40.0000 chunk 77 optimal weight: 0.6980 chunk 386 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 357 optimal weight: 0.8980 chunk 321 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 409 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 690 GLN B 755 GLN C 536 ASN C 804 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN D 373 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.172486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137772 restraints weight = 74141.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.133806 restraints weight = 130445.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131337 restraints weight = 114219.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130324 restraints weight = 114705.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130182 restraints weight = 102821.833| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35560 Z= 0.168 Angle : 0.733 13.422 48531 Z= 0.347 Chirality : 0.048 0.569 5615 Planarity : 0.004 0.046 6112 Dihedral : 8.194 59.680 6502 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 4.68 % Allowed : 20.74 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.12), residues: 4151 helix: 0.41 (0.14), residues: 1342 sheet: -0.56 (0.18), residues: 744 loop : -2.08 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.026 0.001 TYR C 904 PHE 0.023 0.002 PHE D 452 TRP 0.028 0.002 TRP D 203 HIS 0.006 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00395 (35422) covalent geometry : angle 0.70067 (48162) SS BOND : bond 0.00380 ( 45) SS BOND : angle 2.27750 ( 90) hydrogen bonds : bond 0.04354 ( 1287) hydrogen bonds : angle 5.06250 ( 3675) link_BETA1-4 : bond 0.00515 ( 33) link_BETA1-4 : angle 2.34743 ( 99) link_NAG-ASN : bond 0.00496 ( 60) link_NAG-ASN : angle 2.81980 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 279 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8923 (mt) cc_final: 0.8655 (mp) REVERT: A 226 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6813 (tp) REVERT: A 374 PHE cc_start: 0.7454 (m-80) cc_final: 0.7239 (m-10) REVERT: A 902 MET cc_start: 0.8992 (tpt) cc_final: 0.8458 (tpt) REVERT: B 153 MET cc_start: -0.0462 (mpp) cc_final: -0.2137 (ptm) REVERT: B 190 ARG cc_start: 0.6403 (mtt180) cc_final: 0.6061 (mmt180) REVERT: B 546 LEU cc_start: 0.7414 (mp) cc_final: 0.7193 (pp) REVERT: B 1144 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7081 (mt-10) REVERT: C 131 CYS cc_start: 0.4168 (OUTLIER) cc_final: 0.3835 (m) REVERT: C 153 MET cc_start: -0.2014 (mpp) cc_final: -0.4106 (ttm) REVERT: C 202 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8016 (tptm) REVERT: C 619 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: C 693 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8706 (pt) REVERT: D 83 TYR cc_start: 0.3104 (m-80) cc_final: 0.2874 (m-80) REVERT: D 129 THR cc_start: 0.5352 (p) cc_final: 0.5064 (t) REVERT: D 197 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.5111 (pm20) REVERT: D 249 MET cc_start: 0.4840 (mmt) cc_final: 0.3638 (mtt) REVERT: D 270 MET cc_start: 0.4020 (mmm) cc_final: 0.3768 (mmm) REVERT: E 23 GLU cc_start: 0.3203 (OUTLIER) cc_final: 0.2603 (tp30) REVERT: E 90 ASN cc_start: 0.0696 (t0) cc_final: -0.0009 (m110) REVERT: E 177 ARG cc_start: 0.4268 (ttt-90) cc_final: 0.3966 (ttp80) REVERT: E 183 TYR cc_start: 0.2796 (OUTLIER) cc_final: 0.1429 (t80) REVERT: E 190 MET cc_start: 0.0719 (ppp) cc_final: -0.1669 (ttp) REVERT: E 249 MET cc_start: 0.2147 (tpt) cc_final: 0.0616 (mmt) REVERT: E 455 MET cc_start: 0.2626 (ttp) cc_final: 0.2083 (tmm) REVERT: E 458 LYS cc_start: 0.1907 (mmtm) cc_final: 0.1667 (mmmt) REVERT: E 462 MET cc_start: 0.1531 (mtp) cc_final: 0.0580 (mmt) REVERT: E 557 MET cc_start: 0.5055 (ppp) cc_final: 0.4819 (ppp) outliers start: 173 outliers final: 121 residues processed: 425 average time/residue: 0.1770 time to fit residues: 128.3655 Evaluate side-chains 374 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 245 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 913 GLN B 121 ASN C 607 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.172375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142156 restraints weight = 73847.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140343 restraints weight = 133941.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.138282 restraints weight = 121298.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137606 restraints weight = 111430.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136774 restraints weight = 91669.145| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 35560 Z= 0.164 Angle : 0.716 13.171 48531 Z= 0.339 Chirality : 0.048 0.574 5615 Planarity : 0.004 0.046 6112 Dihedral : 7.843 59.867 6498 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.53 % Favored : 93.33 % Rotamer: Outliers : 4.33 % Allowed : 21.33 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.20 (0.13), residues: 4151 helix: 0.62 (0.14), residues: 1350 sheet: -0.35 (0.18), residues: 749 loop : -2.01 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 161 TYR 0.030 0.001 TYR C 904 PHE 0.022 0.002 PHE D 452 TRP 0.020 0.001 TRP D 203 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00385 (35422) covalent geometry : angle 0.68445 (48162) SS BOND : bond 0.00394 ( 45) SS BOND : angle 2.25130 ( 90) hydrogen bonds : bond 0.04174 ( 1287) hydrogen bonds : angle 4.94733 ( 3675) link_BETA1-4 : bond 0.00534 ( 33) link_BETA1-4 : angle 2.34953 ( 99) link_NAG-ASN : bond 0.00369 ( 60) link_NAG-ASN : angle 2.73283 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 268 time to evaluate : 1.090 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 226 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6811 (tp) REVERT: A 374 PHE cc_start: 0.7327 (m-80) cc_final: 0.7126 (m-10) REVERT: A 902 MET cc_start: 0.9035 (tpt) cc_final: 0.8609 (tpt) REVERT: B 153 MET cc_start: -0.0567 (mpp) cc_final: -0.1975 (ttp) REVERT: C 131 CYS cc_start: 0.4281 (OUTLIER) cc_final: 0.3978 (m) REVERT: C 153 MET cc_start: -0.1933 (mpp) cc_final: -0.4059 (ttm) REVERT: C 296 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9114 (tt) REVERT: C 693 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8687 (pt) REVERT: D 83 TYR cc_start: 0.3131 (m-80) cc_final: 0.2813 (m-80) REVERT: D 129 THR cc_start: 0.5139 (p) cc_final: 0.4765 (t) REVERT: D 249 MET cc_start: 0.4672 (mmt) cc_final: 0.3990 (mmt) REVERT: D 270 MET cc_start: 0.3876 (mmm) cc_final: 0.3578 (mmm) REVERT: D 474 MET cc_start: 0.6483 (ptp) cc_final: 0.6080 (pmm) REVERT: E 23 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.2813 (tp30) REVERT: E 90 ASN cc_start: 0.0662 (t0) cc_final: -0.0007 (m110) REVERT: E 177 ARG cc_start: 0.4512 (ttt-90) cc_final: 0.4254 (ttp80) REVERT: E 183 TYR cc_start: 0.3135 (OUTLIER) cc_final: 0.1749 (t80) REVERT: E 190 MET cc_start: 0.1170 (ppp) cc_final: -0.1225 (ttt) REVERT: E 249 MET cc_start: 0.2267 (tpt) cc_final: 0.0700 (mtt) REVERT: E 455 MET cc_start: 0.2839 (ttp) cc_final: 0.2241 (tmm) REVERT: E 462 MET cc_start: 0.1853 (mtp) cc_final: 0.0908 (mmt) REVERT: E 557 MET cc_start: 0.5463 (ppp) cc_final: 0.5239 (ppp) outliers start: 160 outliers final: 122 residues processed: 401 average time/residue: 0.1705 time to fit residues: 118.5449 Evaluate side-chains 366 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 238 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 321 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 690 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.172074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137350 restraints weight = 74121.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133948 restraints weight = 134785.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132241 restraints weight = 114634.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131228 restraints weight = 113355.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131410 restraints weight = 105794.772| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35560 Z= 0.154 Angle : 0.705 12.860 48531 Z= 0.333 Chirality : 0.048 0.565 5615 Planarity : 0.004 0.046 6112 Dihedral : 7.569 59.641 6495 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 4.55 % Allowed : 21.33 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.03 (0.13), residues: 4151 helix: 0.81 (0.15), residues: 1330 sheet: -0.18 (0.19), residues: 744 loop : -1.95 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 482 TYR 0.025 0.001 TYR C 904 PHE 0.026 0.001 PHE D 452 TRP 0.032 0.001 TRP D 203 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00362 (35422) covalent geometry : angle 0.67432 (48162) SS BOND : bond 0.00354 ( 45) SS BOND : angle 2.12071 ( 90) hydrogen bonds : bond 0.04031 ( 1287) hydrogen bonds : angle 4.85588 ( 3675) link_BETA1-4 : bond 0.00572 ( 33) link_BETA1-4 : angle 2.26339 ( 99) link_NAG-ASN : bond 0.00371 ( 60) link_NAG-ASN : angle 2.67424 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 268 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6779 (tp) REVERT: A 374 PHE cc_start: 0.7455 (m-80) cc_final: 0.7201 (m-10) REVERT: A 423 TYR cc_start: 0.6073 (t80) cc_final: 0.5516 (t80) REVERT: A 902 MET cc_start: 0.8948 (tpt) cc_final: 0.8567 (tpt) REVERT: B 153 MET cc_start: -0.0466 (mpp) cc_final: -0.1950 (ttp) REVERT: B 190 ARG cc_start: 0.6809 (mtt180) cc_final: 0.6462 (mtt180) REVERT: B 1144 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7058 (mt-10) REVERT: C 131 CYS cc_start: 0.4349 (OUTLIER) cc_final: 0.3997 (m) REVERT: C 153 MET cc_start: -0.2182 (mpp) cc_final: -0.4183 (ttm) REVERT: C 189 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6033 (tt) REVERT: C 296 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9108 (tt) REVERT: C 421 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.4081 (p90) REVERT: C 455 LEU cc_start: 0.2509 (OUTLIER) cc_final: 0.2274 (tt) REVERT: C 693 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8696 (pt) REVERT: D 83 TYR cc_start: 0.3370 (m-80) cc_final: 0.2883 (m-80) REVERT: D 129 THR cc_start: 0.5221 (p) cc_final: 0.4782 (t) REVERT: D 249 MET cc_start: 0.4724 (mmt) cc_final: 0.4051 (mmt) REVERT: D 332 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7084 (ttp) REVERT: D 536 GLU cc_start: 0.4729 (mp0) cc_final: 0.4383 (mm-30) REVERT: E 23 GLU cc_start: 0.3452 (OUTLIER) cc_final: 0.2700 (tp30) REVERT: E 90 ASN cc_start: 0.0621 (t0) cc_final: -0.0066 (m110) REVERT: E 177 ARG cc_start: 0.4307 (ttt-90) cc_final: 0.3903 (mtp180) REVERT: E 183 TYR cc_start: 0.2670 (OUTLIER) cc_final: 0.1399 (t80) REVERT: E 190 MET cc_start: 0.0885 (ppp) cc_final: -0.1254 (ttt) REVERT: E 249 MET cc_start: 0.2092 (tpt) cc_final: 0.0535 (mtt) REVERT: E 455 MET cc_start: 0.2869 (ttp) cc_final: 0.2452 (tmm) REVERT: E 458 LYS cc_start: 0.1670 (mmtm) cc_final: 0.1450 (mmmt) REVERT: E 462 MET cc_start: 0.1793 (mtp) cc_final: 0.0669 (mmt) REVERT: E 557 MET cc_start: 0.5128 (ppp) cc_final: 0.4901 (ppp) outliers start: 168 outliers final: 132 residues processed: 407 average time/residue: 0.1776 time to fit residues: 123.8189 Evaluate side-chains 381 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 239 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 287 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 325 optimal weight: 30.0000 chunk 293 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 370 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.142574 restraints weight = 74060.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140335 restraints weight = 136786.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.138924 restraints weight = 127959.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137936 restraints weight = 123820.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136669 restraints weight = 117443.312| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35560 Z= 0.128 Angle : 0.682 12.227 48531 Z= 0.323 Chirality : 0.047 0.543 5615 Planarity : 0.004 0.046 6112 Dihedral : 7.231 59.769 6491 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 3.90 % Allowed : 22.01 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.89 (0.13), residues: 4151 helix: 0.91 (0.15), residues: 1333 sheet: -0.05 (0.19), residues: 743 loop : -1.88 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 161 TYR 0.021 0.001 TYR C 904 PHE 0.028 0.001 PHE E 40 TRP 0.028 0.001 TRP D 203 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00293 (35422) covalent geometry : angle 0.65365 (48162) SS BOND : bond 0.00394 ( 45) SS BOND : angle 1.95340 ( 90) hydrogen bonds : bond 0.03748 ( 1287) hydrogen bonds : angle 4.75602 ( 3675) link_BETA1-4 : bond 0.00587 ( 33) link_BETA1-4 : angle 2.20903 ( 99) link_NAG-ASN : bond 0.00356 ( 60) link_NAG-ASN : angle 2.52617 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 262 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6697 (tp) REVERT: A 423 TYR cc_start: 0.5940 (t80) cc_final: 0.5551 (t80) REVERT: A 902 MET cc_start: 0.9209 (tpt) cc_final: 0.8976 (tpt) REVERT: B 153 MET cc_start: -0.0742 (mpp) cc_final: -0.2042 (ttp) REVERT: B 190 ARG cc_start: 0.6748 (mtt180) cc_final: 0.6426 (mtt180) REVERT: C 131 CYS cc_start: 0.4592 (OUTLIER) cc_final: 0.4224 (m) REVERT: C 153 MET cc_start: -0.2189 (mpp) cc_final: -0.4199 (ttm) REVERT: C 235 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7545 (tp) REVERT: C 296 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9100 (tt) REVERT: C 588 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (p) REVERT: C 693 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8723 (pt) REVERT: C 787 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: D 82 MET cc_start: 0.6141 (mpp) cc_final: 0.5536 (mmt) REVERT: D 83 TYR cc_start: 0.3288 (m-80) cc_final: 0.2792 (m-80) REVERT: D 129 THR cc_start: 0.4859 (p) cc_final: 0.4361 (t) REVERT: D 249 MET cc_start: 0.4811 (mmt) cc_final: 0.4179 (mmt) REVERT: D 536 GLU cc_start: 0.4403 (mp0) cc_final: 0.4147 (mm-30) REVERT: E 23 GLU cc_start: 0.3338 (OUTLIER) cc_final: 0.2673 (tp30) REVERT: E 90 ASN cc_start: 0.0571 (t0) cc_final: -0.0112 (m110) REVERT: E 177 ARG cc_start: 0.4412 (ttt-90) cc_final: 0.4169 (ttp80) REVERT: E 183 TYR cc_start: 0.3023 (OUTLIER) cc_final: 0.1685 (t80) REVERT: E 190 MET cc_start: 0.0908 (ppp) cc_final: -0.1374 (ttt) REVERT: E 249 MET cc_start: 0.2109 (tpt) cc_final: 0.0577 (mtt) REVERT: E 462 MET cc_start: 0.1889 (mtp) cc_final: 0.0781 (mmt) outliers start: 144 outliers final: 107 residues processed: 380 average time/residue: 0.1751 time to fit residues: 114.0723 Evaluate side-chains 353 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 237 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 225 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 416 optimal weight: 4.9990 chunk 377 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 191 optimal weight: 0.0870 chunk 290 optimal weight: 6.9990 chunk 315 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 239 GLN C 360 ASN C 907 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.170785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140697 restraints weight = 73765.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137834 restraints weight = 128339.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136703 restraints weight = 126507.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135752 restraints weight = 122220.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.133754 restraints weight = 112693.107| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 35560 Z= 0.206 Angle : 0.755 13.238 48531 Z= 0.358 Chirality : 0.049 0.576 5615 Planarity : 0.004 0.046 6112 Dihedral : 7.536 59.975 6489 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.20 % Favored : 92.70 % Rotamer: Outliers : 3.98 % Allowed : 22.04 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.13), residues: 4151 helix: 0.82 (0.15), residues: 1329 sheet: -0.17 (0.19), residues: 732 loop : -1.95 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.027 0.002 TYR C 904 PHE 0.032 0.002 PHE E 40 TRP 0.045 0.002 TRP E 461 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00494 (35422) covalent geometry : angle 0.72554 (48162) SS BOND : bond 0.00379 ( 45) SS BOND : angle 2.28691 ( 90) hydrogen bonds : bond 0.04319 ( 1287) hydrogen bonds : angle 4.94270 ( 3675) link_BETA1-4 : bond 0.00537 ( 33) link_BETA1-4 : angle 2.33141 ( 99) link_NAG-ASN : bond 0.00408 ( 60) link_NAG-ASN : angle 2.70411 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 242 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6811 (tp) REVERT: A 423 TYR cc_start: 0.5942 (t80) cc_final: 0.5612 (t80) REVERT: A 902 MET cc_start: 0.9045 (tpt) cc_final: 0.8528 (tpt) REVERT: B 153 MET cc_start: -0.0788 (mpp) cc_final: -0.2339 (ptm) REVERT: B 190 ARG cc_start: 0.6785 (mtt180) cc_final: 0.6460 (mtt180) REVERT: C 153 MET cc_start: -0.2042 (mpp) cc_final: -0.4021 (ttm) REVERT: C 296 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9111 (tt) REVERT: C 693 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8760 (pt) REVERT: C 787 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: D 83 TYR cc_start: 0.3201 (m-80) cc_final: 0.2935 (m-80) REVERT: D 129 THR cc_start: 0.5157 (p) cc_final: 0.4599 (t) REVERT: D 249 MET cc_start: 0.4808 (mmt) cc_final: 0.3891 (mmp) REVERT: D 270 MET cc_start: 0.3627 (mmm) cc_final: 0.3300 (mmt) REVERT: E 23 GLU cc_start: 0.3525 (OUTLIER) cc_final: 0.2744 (tp30) REVERT: E 90 ASN cc_start: 0.0671 (t0) cc_final: -0.0026 (m110) REVERT: E 183 TYR cc_start: 0.3212 (OUTLIER) cc_final: 0.1730 (t80) REVERT: E 190 MET cc_start: 0.1107 (ppp) cc_final: -0.1173 (ttt) REVERT: E 249 MET cc_start: 0.2297 (tpt) cc_final: 0.0731 (mtt) REVERT: E 462 MET cc_start: 0.1578 (mtp) cc_final: 0.0903 (mmt) outliers start: 147 outliers final: 122 residues processed: 366 average time/residue: 0.1746 time to fit residues: 110.2233 Evaluate side-chains 359 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 231 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 186 optimal weight: 0.7980 chunk 351 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.172558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.143036 restraints weight = 74034.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140911 restraints weight = 137635.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.139217 restraints weight = 128021.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138808 restraints weight = 122699.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137743 restraints weight = 106369.905| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35560 Z= 0.126 Angle : 0.707 12.093 48531 Z= 0.337 Chirality : 0.047 0.547 5615 Planarity : 0.004 0.046 6112 Dihedral : 7.231 59.899 6485 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 3.28 % Allowed : 22.77 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.86 (0.13), residues: 4151 helix: 0.94 (0.15), residues: 1329 sheet: -0.02 (0.19), residues: 729 loop : -1.85 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 177 TYR 0.048 0.001 TYR A 160 PHE 0.051 0.001 PHE C 392 TRP 0.066 0.002 TRP E 461 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00281 (35422) covalent geometry : angle 0.67968 (48162) SS BOND : bond 0.00473 ( 45) SS BOND : angle 1.97181 ( 90) hydrogen bonds : bond 0.03810 ( 1287) hydrogen bonds : angle 4.80958 ( 3675) link_BETA1-4 : bond 0.00551 ( 33) link_BETA1-4 : angle 2.20221 ( 99) link_NAG-ASN : bond 0.00349 ( 60) link_NAG-ASN : angle 2.53307 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 245 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6687 (tp) REVERT: A 423 TYR cc_start: 0.5896 (t80) cc_final: 0.5605 (t80) REVERT: A 902 MET cc_start: 0.8998 (tpt) cc_final: 0.8693 (tpt) REVERT: B 153 MET cc_start: -0.0343 (mpp) cc_final: -0.1971 (ptm) REVERT: B 190 ARG cc_start: 0.6703 (mtt180) cc_final: 0.6378 (mtt180) REVERT: B 1144 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6754 (mt-10) REVERT: C 153 MET cc_start: -0.2216 (mpp) cc_final: -0.4220 (ttm) REVERT: C 296 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9110 (tt) REVERT: C 524 VAL cc_start: 0.6526 (OUTLIER) cc_final: 0.6322 (p) REVERT: C 693 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8733 (pt) REVERT: C 787 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: D 82 MET cc_start: 0.6180 (mpp) cc_final: 0.5584 (mmt) REVERT: D 83 TYR cc_start: 0.3116 (m-80) cc_final: 0.2821 (m-80) REVERT: D 129 THR cc_start: 0.5052 (p) cc_final: 0.4524 (t) REVERT: D 249 MET cc_start: 0.4883 (mmt) cc_final: 0.4243 (mmt) REVERT: D 323 MET cc_start: 0.3185 (mmm) cc_final: 0.2894 (mmm) REVERT: D 475 LYS cc_start: 0.6761 (tttm) cc_final: 0.6433 (mtpp) REVERT: D 536 GLU cc_start: 0.4503 (mp0) cc_final: 0.4051 (mm-30) REVERT: E 23 GLU cc_start: 0.3345 (OUTLIER) cc_final: 0.2550 (tp30) REVERT: E 90 ASN cc_start: 0.0604 (t0) cc_final: -0.0046 (m110) REVERT: E 183 TYR cc_start: 0.3159 (OUTLIER) cc_final: 0.1760 (t80) REVERT: E 190 MET cc_start: 0.0758 (ppp) cc_final: -0.1530 (ttt) REVERT: E 249 MET cc_start: 0.2124 (tpt) cc_final: 0.0635 (mtt) REVERT: E 462 MET cc_start: 0.1530 (mtp) cc_final: 0.0872 (mmt) outliers start: 121 outliers final: 105 residues processed: 350 average time/residue: 0.1806 time to fit residues: 108.6944 Evaluate side-chains 344 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 232 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 319 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 327 optimal weight: 0.0070 chunk 222 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 211 optimal weight: 0.0980 chunk 264 optimal weight: 9.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN C 394 ASN D 373 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.172786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.143492 restraints weight = 73416.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140444 restraints weight = 129793.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138427 restraints weight = 128151.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137528 restraints weight = 112146.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136288 restraints weight = 103109.870| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35560 Z= 0.123 Angle : 0.684 11.731 48531 Z= 0.325 Chirality : 0.047 0.527 5615 Planarity : 0.004 0.047 6112 Dihedral : 6.928 59.952 6485 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 3.06 % Allowed : 23.06 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.76 (0.13), residues: 4151 helix: 0.98 (0.15), residues: 1347 sheet: 0.11 (0.19), residues: 735 loop : -1.81 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.025 0.001 TYR C 904 PHE 0.026 0.001 PHE E 40 TRP 0.056 0.002 TRP E 461 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00278 (35422) covalent geometry : angle 0.65887 (48162) SS BOND : bond 0.00317 ( 45) SS BOND : angle 1.84132 ( 90) hydrogen bonds : bond 0.03604 ( 1287) hydrogen bonds : angle 4.71422 ( 3675) link_BETA1-4 : bond 0.00577 ( 33) link_BETA1-4 : angle 2.14673 ( 99) link_NAG-ASN : bond 0.00350 ( 60) link_NAG-ASN : angle 2.42106 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5788.78 seconds wall clock time: 100 minutes 42.70 seconds (6042.70 seconds total)