Starting phenix.real_space_refine on Wed Apr 8 15:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v89_31794/04_2026/7v89_31794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v89_31794/04_2026/7v89_31794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v89_31794/04_2026/7v89_31794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v89_31794/04_2026/7v89_31794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v89_31794/04_2026/7v89_31794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v89_31794/04_2026/7v89_31794.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.060 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 195 5.16 5 C 25472 2.51 5 N 6535 2.21 5 O 7832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40034 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "C" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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 Time building chain proxies: 10.00, per 1000 atoms: 0.25 Number of scatterers: 40034 At special positions: 0 Unit cell: (176, 150.7, 245.3, 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 195 16.00 O 7832 8.00 N 6535 7.00 C 25472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.04 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 341 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 601 " " NAG C2003 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 432 " " NAG H2001 " - " ASN H 53 " " NAG H2002 " - " ASN H 90 " " NAG I 1 " - " ASN A 232 " " NAG J 1 " - " ASN A 280 " " NAG K 1 " - " ASN A 329 " " NAG L 1 " - " ASN A 341 " " NAG M 1 " - " ASN A 614 " " NAG N 1 " - " ASN A 707 " " NAG O 1 " - " ASN A 715 " " NAG P 1 " - " ASN A 799 " " NAG Q 1 " - " ASN A1072 " " NAG R 1 " - " ASN A1096 " " NAG S 1 " - " ASN A1132 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 163 " " NAG V 1 " - " ASN B 232 " " NAG W 1 " - " ASN B 280 " " NAG X 1 " - " ASN B 329 " " NAG Y 1 " - " ASN B 614 " " NAG Z 1 " - " ASN B 707 " " NAG a 1 " - " ASN B 715 " " NAG b 1 " - " ASN B 799 " " NAG c 1 " - " ASN B1072 " " NAG d 1 " - " ASN B1096 " " NAG e 1 " - " ASN B1132 " " NAG f 1 " - " ASN C 122 " " NAG g 1 " - " ASN C 163 " " NAG h 1 " - " ASN C 232 " " NAG i 1 " - " ASN C 280 " " NAG j 1 " - " ASN C 329 " " NAG k 1 " - " ASN C 341 " " NAG l 1 " - " ASN C 614 " " NAG m 1 " - " ASN C 707 " " NAG n 1 " - " ASN C 715 " " NAG o 1 " - " ASN C 799 " " NAG p 1 " - " ASN C1072 " " NAG q 1 " - " ASN C1096 " " NAG r 1 " - " ASN C1132 " " NAG s 1 " - " ASN F 90 " " NAG t 1 " - " ASN F 103 " " NAG u 1 " - " ASN F 322 " " NAG v 1 " - " ASN F 546 " " NAG w 1 " - " ASN H 322 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9156 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 54 sheets defined 40.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.278A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.533A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.661A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.329A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.586A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.532A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.952A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.833A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.508A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.978A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.197A pdb=" N ASN B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.037A pdb=" N TYR B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 757 through 781 removed outlier: 3.659A pdb=" N LEU B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.580A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 910 through 939 removed outlier: 4.266A pdb=" N LEU B 914 " --> pdb=" O THR B 910 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS B 919 " --> pdb=" O TYR B 915 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 920 " --> pdb=" O GLU B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.551A pdb=" N GLN B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 981 removed outlier: 3.517A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 5.015A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.922A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.589A pdb=" N VAL C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.510A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.375A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.916A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.262A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.562A pdb=" N SER C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 removed outlier: 3.729A pdb=" N TYR C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.131A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 781 Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.553A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.554A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 916 removed outlier: 4.191A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.588A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.088A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.559A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.533A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.726A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 103 through 107 removed outlier: 4.057A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 194 removed outlier: 3.748A pdb=" N LEU F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.896A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.605A pdb=" N LEU F 266 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 263 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.570A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.599A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.888A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 413 removed outlier: 3.989A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.147A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.561A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.709A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.415A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.868A pdb=" N CYS F 542 " --> pdb=" O LEU F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.586A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 3.968A pdb=" N SER F 563 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 560 through 564' Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.975A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.612A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 79 removed outlier: 3.707A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 removed outlier: 3.600A pdb=" N ALA G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.536A pdb=" N SER G 106 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.565A pdb=" N LEU G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 194 removed outlier: 4.495A pdb=" N LEU G 179 " --> pdb=" O GLN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 205 removed outlier: 3.857A pdb=" N TYR G 202 " --> pdb=" O ASP G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 218 through 229 removed outlier: 3.652A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 252 Processing helix chain 'G' and resid 264 through 268 removed outlier: 4.163A pdb=" N GLY G 268 " --> pdb=" O HIS G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 293 through 301 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 385 Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 397 through 412 removed outlier: 4.051A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 447 removed outlier: 3.849A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.561A pdb=" N ARG G 482 " --> pdb=" O TRP G 478 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 507 removed outlier: 3.505A pdb=" N VAL G 506 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER G 507 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 507' Processing helix chain 'G' and resid 512 through 532 removed outlier: 3.944A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 519 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU G 520 " --> pdb=" O TYR G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.877A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.723A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN G 599 " --> pdb=" O LEU G 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.988A pdb=" N GLU H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 79 removed outlier: 3.821A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.974A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 158 through 172 Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.376A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 218 through 229 removed outlier: 3.513A pdb=" N LEU H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 233 through 252 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 293 through 300 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 Processing helix chain 'H' and resid 365 through 386 Processing helix chain 'H' and resid 387 through 388 No H-bonds generated for 'chain 'H' and resid 387 through 388' Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.698A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 413 removed outlier: 4.258A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.767A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 removed outlier: 3.707A pdb=" N TRP H 477 " --> pdb=" O TRP H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.516A pdb=" N SER H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN H 508 " --> pdb=" O PHE H 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 503 through 508' Processing helix chain 'H' and resid 512 through 532 removed outlier: 4.112A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.657A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 removed outlier: 3.785A pdb=" N SER H 563 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 560 through 564' Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.535A pdb=" N LEU H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 597 removed outlier: 4.200A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.970A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.638A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 540 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.033A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.096A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLU A 132 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLN A 134 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ASN A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.596A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.787A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.766A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.289A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.703A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.595A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.464A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1092 through 1095 removed outlier: 4.792A pdb=" N GLN A1104 " --> pdb=" O GLU A1109 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU A1109 " --> pdb=" O GLN A1104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.963A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.084A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.125A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.572A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 323 through 324 removed outlier: 3.536A pdb=" N ASN B 540 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.747A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC9, first strand: chain 'B' and resid 571 through 574 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.309A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.888A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 726 removed outlier: 3.590A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.440A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD7, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 4.723A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.091A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.251A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.574A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE4, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.770A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE6, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE7, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.221A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.550A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.530A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF3, first strand: chain 'C' and resid 1092 through 1094 removed outlier: 4.769A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF5, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.258A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 132 through 133 Processing sheet with id=AF7, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AF8, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.174A pdb=" N ASN H 134 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU H 140 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 347 through 350 1737 hydrogen bonds defined for protein. 4869 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: 10.22 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12708 1.34 - 1.46: 10214 1.46 - 1.58: 17783 1.58 - 1.70: 1 1.70 - 1.82: 282 Bond restraints: 40988 Sorted by residual: bond pdb=" CB PRO G 253 " pdb=" CG PRO G 253 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" C1 NAG p 1 " pdb=" O5 NAG p 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 40983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 55079 2.30 - 4.59: 594 4.59 - 6.89: 55 6.89 - 9.19: 10 9.19 - 11.49: 3 Bond angle restraints: 55741 Sorted by residual: angle pdb=" CA PRO G 253 " pdb=" N PRO G 253 " pdb=" CD PRO G 253 " ideal model delta sigma weight residual 112.00 101.36 10.64 1.40e+00 5.10e-01 5.78e+01 angle pdb=" N MET F 123 " pdb=" CA MET F 123 " pdb=" CB MET F 123 " ideal model delta sigma weight residual 110.30 117.23 -6.93 1.54e+00 4.22e-01 2.02e+01 angle pdb=" CA MET F 123 " pdb=" CB MET F 123 " pdb=" CG MET F 123 " ideal model delta sigma weight residual 114.10 122.55 -8.45 2.00e+00 2.50e-01 1.78e+01 angle pdb=" CB MET F 123 " pdb=" CG MET F 123 " pdb=" SD MET F 123 " ideal model delta sigma weight residual 112.70 124.19 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C THR F 122 " pdb=" N MET F 123 " pdb=" CA MET F 123 " ideal model delta sigma weight residual 120.68 114.21 6.47 1.70e+00 3.46e-01 1.45e+01 ... (remaining 55736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 23621 21.15 - 42.30: 1688 42.30 - 63.45: 259 63.45 - 84.60: 71 84.60 - 105.75: 20 Dihedral angle restraints: 25659 sinusoidal: 11442 harmonic: 14217 Sorted by residual: dihedral pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " pdb=" SG CYS B 758 " pdb=" CB CYS B 758 " ideal model delta sinusoidal sigma weight residual -86.00 3.30 -89.30 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 1.64 -87.64 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C 289 " pdb=" SG CYS C 289 " pdb=" SG CYS C 299 " pdb=" CB CYS C 299 " ideal model delta sinusoidal sigma weight residual -86.00 -172.93 86.93 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 25656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 6431 0.186 - 0.373: 5 0.373 - 0.559: 0 0.559 - 0.746: 0 0.746 - 0.932: 1 Chirality restraints: 6437 Sorted by residual: chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN C1096 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG v 1 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG v 1 " pdb=" O5 NAG v 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA PRO G 253 " pdb=" N PRO G 253 " pdb=" C PRO G 253 " pdb=" CB PRO G 253 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 6434 not shown) Planarity restraints: 7144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 252 " 0.062 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO G 253 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO G 253 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 253 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 25 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 26 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 134 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO H 135 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 135 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 135 " -0.029 5.00e-02 4.00e+02 ... (remaining 7141 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 900 2.68 - 3.24: 39186 3.24 - 3.79: 63024 3.79 - 4.35: 81668 4.35 - 4.90: 135186 Nonbonded interactions: 319964 Sorted by model distance: nonbonded pdb=" OG SER B 347 " pdb=" O ARG B 450 " model vdw 2.128 3.040 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.159 3.040 nonbonded pdb=" NH2 ARG F 482 " pdb=" O THR F 608 " model vdw 2.162 3.120 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.175 3.040 ... (remaining 319959 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' selection = (chain 'B' and resid 14 through 2003) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' 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' } ncs_group { reference = (chain 'F' and resid 19 through 614) selection = chain 'G' selection = (chain 'H' and resid 19 through 614) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.570 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 51.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.003 0.162 41136 Z= 0.164 Angle : 0.604 15.108 56137 Z= 0.292 Chirality : 0.045 0.932 6437 Planarity : 0.004 0.087 7087 Dihedral : 14.389 105.748 16359 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.26 (0.12), residues: 4815 helix: 1.83 (0.13), residues: 1669 sheet: 0.43 (0.18), residues: 749 loop : -1.16 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 192 TYR 0.014 0.001 TYR A1065 PHE 0.030 0.001 PHE F 369 TRP 0.012 0.001 TRP F 69 HIS 0.012 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00338 (40988) covalent geometry : angle 0.57827 (55741) SS BOND : bond 0.00246 ( 48) SS BOND : angle 1.01224 ( 96) hydrogen bonds : bond 0.13003 ( 1737) hydrogen bonds : angle 5.37198 ( 4869) link_BETA1-4 : bond 0.00377 ( 43) link_BETA1-4 : angle 2.14298 ( 129) link_NAG-ASN : bond 0.00311 ( 57) link_NAG-ASN : angle 2.59251 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6240 (ttt90) REVERT: A 451 TYR cc_start: 0.7032 (p90) cc_final: 0.5931 (p90) REVERT: A 641 PHE cc_start: 0.7867 (t80) cc_final: 0.7611 (t80) REVERT: B 572 ASP cc_start: 0.7418 (m-30) cc_final: 0.7049 (m-30) REVERT: C 133 PHE cc_start: 0.7539 (m-80) cc_final: 0.7298 (m-80) REVERT: C 367 TYR cc_start: 0.8685 (t80) cc_final: 0.8295 (t80) REVERT: C 368 ASN cc_start: 0.8024 (m-40) cc_final: 0.7781 (p0) REVERT: C 513 PHE cc_start: 0.7334 (m-80) cc_final: 0.6926 (m-80) REVERT: F 123 MET cc_start: 0.8019 (pmm) cc_final: 0.7595 (ppp) REVERT: F 480 MET cc_start: 0.7727 (mpp) cc_final: 0.7403 (mpp) REVERT: F 527 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7644 (tp30) REVERT: G 26 LYS cc_start: 0.6277 (mttt) cc_final: 0.5954 (tppt) REVERT: G 152 MET cc_start: 0.0169 (ptt) cc_final: -0.0239 (mtp) REVERT: G 171 GLU cc_start: 0.1594 (pp20) cc_final: 0.1243 (mp0) REVERT: G 227 GLU cc_start: 0.4993 (pm20) cc_final: 0.4181 (pp20) REVERT: G 462 MET cc_start: 0.1739 (ptt) cc_final: 0.1350 (ptp) REVERT: G 557 MET cc_start: 0.0646 (ttt) cc_final: 0.0349 (ptm) REVERT: G 573 VAL cc_start: 0.2416 (t) cc_final: 0.1750 (p) REVERT: G 581 VAL cc_start: 0.2408 (p) cc_final: 0.2056 (p) REVERT: G 586 ASN cc_start: 0.3753 (m-40) cc_final: 0.3084 (m-40) REVERT: H 111 ASP cc_start: 0.8482 (m-30) cc_final: 0.8251 (t70) REVERT: H 152 MET cc_start: 0.0266 (tmm) cc_final: -0.0106 (ttm) REVERT: H 297 MET cc_start: 0.2287 (pmm) cc_final: 0.1812 (pmm) REVERT: H 366 MET cc_start: 0.4107 (tpt) cc_final: 0.3718 (OUTLIER) REVERT: H 462 MET cc_start: 0.7631 (ptp) cc_final: 0.7251 (mmt) REVERT: H 474 MET cc_start: 0.1865 (ppp) cc_final: 0.0929 (ppp) REVERT: H 557 MET cc_start: 0.7439 (ppp) cc_final: 0.6787 (ppp) REVERT: H 572 ASN cc_start: 0.6787 (m-40) cc_final: 0.6192 (p0) REVERT: H 579 MET cc_start: 0.2622 (tpp) cc_final: 0.2261 (tpp) outliers start: 0 outliers final: 1 residues processed: 369 average time/residue: 0.6988 time to fit residues: 315.8926 Evaluate side-chains 205 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 20.0000 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 448 ASN A 912 ASN B 802 GLN B 899 GLN C 115 GLN C 332 ASN C 412 GLN C 540 ASN C 912 ASN C 955 GLN C1003 GLN C1104 GLN F 34 HIS F 442 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN H 531 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.181345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110761 restraints weight = 77024.062| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 4.79 r_work: 0.2990 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 41136 Z= 0.253 Angle : 0.700 11.703 56137 Z= 0.347 Chirality : 0.048 0.272 6437 Planarity : 0.005 0.062 7087 Dihedral : 7.838 88.918 7323 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 1.10 % Allowed : 8.97 % Favored : 89.93 % 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: 0.13 (0.12), residues: 4815 helix: 1.63 (0.13), residues: 1709 sheet: 0.39 (0.19), residues: 720 loop : -1.20 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1037 TYR 0.029 0.002 TYR C1065 PHE 0.047 0.002 PHE A 904 TRP 0.024 0.001 TRP A 884 HIS 0.007 0.002 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00634 (40988) covalent geometry : angle 0.67928 (55741) SS BOND : bond 0.00523 ( 48) SS BOND : angle 1.92460 ( 96) hydrogen bonds : bond 0.06291 ( 1737) hydrogen bonds : angle 4.83091 ( 4869) link_BETA1-4 : bond 0.00340 ( 43) link_BETA1-4 : angle 1.95004 ( 129) link_NAG-ASN : bond 0.00347 ( 57) link_NAG-ASN : angle 2.31872 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8869 (m-30) cc_final: 0.8586 (t0) REVERT: A 456 LYS cc_start: 0.8005 (mppt) cc_final: 0.7602 (mptt) REVERT: A 641 PHE cc_start: 0.8236 (t80) cc_final: 0.7954 (t80) REVERT: A 774 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8714 (ttpt) REVERT: B 572 ASP cc_start: 0.7647 (m-30) cc_final: 0.6958 (m-30) REVERT: B 584 ASP cc_start: 0.7958 (t0) cc_final: 0.7429 (t0) REVERT: C 133 PHE cc_start: 0.7752 (m-80) cc_final: 0.7480 (m-80) REVERT: C 171 GLN cc_start: 0.8802 (mp10) cc_final: 0.7801 (tm130) REVERT: C 367 TYR cc_start: 0.8803 (t80) cc_final: 0.8370 (t80) REVERT: C 368 ASN cc_start: 0.8104 (m-40) cc_final: 0.7777 (p0) REVERT: C 446 ASN cc_start: 0.7348 (t0) cc_final: 0.6759 (t0) REVERT: C 450 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7250 (ptm160) REVERT: C 513 PHE cc_start: 0.7510 (m-80) cc_final: 0.6974 (m-80) REVERT: C 584 ASP cc_start: 0.8317 (t0) cc_final: 0.8106 (m-30) REVERT: C 738 MET cc_start: 0.9054 (ttt) cc_final: 0.8685 (ttt) REVERT: F 123 MET cc_start: 0.8139 (pmm) cc_final: 0.7872 (ppp) REVERT: F 480 MET cc_start: 0.7217 (mpp) cc_final: 0.6948 (mpp) REVERT: G 26 LYS cc_start: 0.6451 (mttt) cc_final: 0.6079 (tppt) REVERT: G 152 MET cc_start: -0.0045 (ptt) cc_final: -0.0396 (mtp) REVERT: G 171 GLU cc_start: 0.1889 (pp20) cc_final: 0.1684 (mp0) REVERT: G 227 GLU cc_start: 0.4807 (pm20) cc_final: 0.4430 (pp20) REVERT: G 360 MET cc_start: 0.1172 (tpp) cc_final: 0.0115 (ptm) REVERT: G 462 MET cc_start: 0.1781 (ptt) cc_final: 0.1533 (ptp) REVERT: G 480 MET cc_start: 0.2737 (pp-130) cc_final: 0.2503 (pp-130) REVERT: G 557 MET cc_start: 0.0440 (ttt) cc_final: 0.0197 (ptm) REVERT: G 573 VAL cc_start: 0.1553 (t) cc_final: 0.0732 (p) REVERT: H 152 MET cc_start: 0.0224 (tmm) cc_final: -0.0120 (ttm) REVERT: H 297 MET cc_start: 0.2468 (pmm) cc_final: 0.2073 (pmm) REVERT: H 323 MET cc_start: 0.4433 (tmm) cc_final: 0.4073 (ttp) REVERT: H 366 MET cc_start: 0.4346 (tpt) cc_final: 0.3833 (OUTLIER) REVERT: H 462 MET cc_start: 0.7648 (ptp) cc_final: 0.7196 (mmt) REVERT: H 474 MET cc_start: 0.2205 (ppp) cc_final: 0.1169 (ppp) REVERT: H 557 MET cc_start: 0.7500 (ppp) cc_final: 0.6806 (ppp) REVERT: H 572 ASN cc_start: 0.6741 (m-40) cc_final: 0.6161 (p0) REVERT: H 579 MET cc_start: 0.2979 (tpp) cc_final: 0.2709 (tpp) outliers start: 47 outliers final: 26 residues processed: 241 average time/residue: 0.6790 time to fit residues: 202.0058 Evaluate side-chains 203 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 774 LYS Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 270 MET Chi-restraints excluded: chain G residue 295 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 196 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 358 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 341 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 368 optimal weight: 40.0000 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 899 GLN G 239 HIS ** G 345 HIS ** 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 = 0.4556 r_free = 0.4556 target = 0.182476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.110322 restraints weight = 77072.301| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.79 r_work: 0.3052 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 41136 Z= 0.132 Angle : 0.592 14.082 56137 Z= 0.290 Chirality : 0.044 0.253 6437 Planarity : 0.004 0.058 7087 Dihedral : 7.180 83.550 7323 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 1.05 % Allowed : 10.65 % Favored : 88.30 % 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: 0.21 (0.12), residues: 4815 helix: 1.70 (0.13), residues: 1720 sheet: 0.50 (0.19), residues: 713 loop : -1.19 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1037 TYR 0.024 0.001 TYR H 385 PHE 0.030 0.001 PHE F 369 TRP 0.018 0.001 TRP A 884 HIS 0.007 0.001 HIS F 373 Details of bonding type rmsd covalent geometry : bond 0.00305 (40988) covalent geometry : angle 0.57240 (55741) SS BOND : bond 0.00329 ( 48) SS BOND : angle 1.45327 ( 96) hydrogen bonds : bond 0.04970 ( 1737) hydrogen bonds : angle 4.60474 ( 4869) link_BETA1-4 : bond 0.00395 ( 43) link_BETA1-4 : angle 1.92443 ( 129) link_NAG-ASN : bond 0.00281 ( 57) link_NAG-ASN : angle 2.06539 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8814 (m-30) cc_final: 0.8579 (t0) REVERT: A 450 ARG cc_start: 0.7961 (mtm180) cc_final: 0.6572 (ttt90) REVERT: A 456 LYS cc_start: 0.8215 (mppt) cc_final: 0.7911 (mptt) REVERT: A 641 PHE cc_start: 0.8138 (t80) cc_final: 0.7861 (t80) REVERT: A 876 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 572 ASP cc_start: 0.7603 (m-30) cc_final: 0.6930 (m-30) REVERT: C 133 PHE cc_start: 0.7832 (m-80) cc_final: 0.7523 (m-80) REVERT: C 171 GLN cc_start: 0.8845 (mp10) cc_final: 0.7838 (tm130) REVERT: C 198 TYR cc_start: 0.8691 (m-80) cc_final: 0.8309 (m-80) REVERT: C 367 TYR cc_start: 0.8821 (t80) cc_final: 0.8416 (t80) REVERT: C 368 ASN cc_start: 0.8150 (m-40) cc_final: 0.7855 (p0) REVERT: C 423 LEU cc_start: 0.8175 (mm) cc_final: 0.7865 (mm) REVERT: C 446 ASN cc_start: 0.7235 (t0) cc_final: 0.6577 (t0) REVERT: C 450 ARG cc_start: 0.7291 (mtm180) cc_final: 0.7018 (ptm160) REVERT: C 584 ASP cc_start: 0.8259 (t0) cc_final: 0.8029 (m-30) REVERT: F 123 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7905 (ppp) REVERT: F 527 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7984 (tp30) REVERT: G 26 LYS cc_start: 0.6452 (mttt) cc_final: 0.6084 (tppt) REVERT: G 152 MET cc_start: -0.0213 (ptt) cc_final: -0.0463 (mtp) REVERT: G 227 GLU cc_start: 0.4617 (pm20) cc_final: 0.4202 (pp20) REVERT: G 360 MET cc_start: 0.1136 (tpp) cc_final: -0.0014 (ptm) REVERT: G 462 MET cc_start: 0.1741 (ptt) cc_final: 0.1511 (ptp) REVERT: G 557 MET cc_start: 0.0250 (ttt) cc_final: 0.0024 (ptm) REVERT: G 573 VAL cc_start: 0.1331 (t) cc_final: 0.0397 (p) REVERT: H 152 MET cc_start: -0.0034 (tmm) cc_final: -0.0276 (ttm) REVERT: H 297 MET cc_start: 0.2369 (pmm) cc_final: 0.2060 (pmm) REVERT: H 323 MET cc_start: 0.4462 (tmm) cc_final: 0.3630 (ppp) REVERT: H 366 MET cc_start: 0.4300 (tpt) cc_final: 0.3846 (OUTLIER) REVERT: H 462 MET cc_start: 0.7591 (ptp) cc_final: 0.7227 (mmt) REVERT: H 474 MET cc_start: 0.2167 (ppp) cc_final: 0.0876 (ppp) REVERT: H 557 MET cc_start: 0.7610 (ppp) cc_final: 0.6917 (ppp) REVERT: H 572 ASN cc_start: 0.6798 (m-40) cc_final: 0.6319 (p0) REVERT: H 579 MET cc_start: 0.3063 (tpp) cc_final: 0.2632 (tpp) outliers start: 45 outliers final: 24 residues processed: 235 average time/residue: 0.7027 time to fit residues: 203.6910 Evaluate side-chains 208 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain G residue 239 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 136 optimal weight: 50.0000 chunk 187 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 385 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 447 optimal weight: 20.0000 chunk 179 optimal weight: 0.4980 chunk 313 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 ASN A 899 GLN B 854 ASN B 899 GLN C1003 GLN F 345 HIS G 250 ASN ** G 345 HIS ** 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 = 0.4540 r_free = 0.4540 target = 0.180623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.114678 restraints weight = 76746.374| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.92 r_work: 0.3011 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 41136 Z= 0.269 Angle : 0.690 17.079 56137 Z= 0.339 Chirality : 0.048 0.253 6437 Planarity : 0.005 0.060 7087 Dihedral : 7.195 80.311 7323 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 1.87 % Allowed : 12.76 % Favored : 85.37 % 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: 0.01 (0.12), residues: 4815 helix: 1.54 (0.13), residues: 1713 sheet: 0.39 (0.19), residues: 709 loop : -1.30 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1037 TYR 0.028 0.002 TYR C1065 PHE 0.029 0.002 PHE F 369 TRP 0.023 0.001 TRP A 884 HIS 0.018 0.002 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00672 (40988) covalent geometry : angle 0.66923 (55741) SS BOND : bond 0.00479 ( 48) SS BOND : angle 1.76519 ( 96) hydrogen bonds : bond 0.06373 ( 1737) hydrogen bonds : angle 4.73987 ( 4869) link_BETA1-4 : bond 0.00343 ( 43) link_BETA1-4 : angle 2.08981 ( 129) link_NAG-ASN : bond 0.00342 ( 57) link_NAG-ASN : angle 2.30223 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 187 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: A 196 ASP cc_start: 0.8833 (m-30) cc_final: 0.8560 (t0) REVERT: A 876 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8837 (tt) REVERT: A 986 GLU cc_start: 0.8896 (mp0) cc_final: 0.8531 (mp0) REVERT: B 572 ASP cc_start: 0.7677 (m-30) cc_final: 0.6957 (m-30) REVERT: B 584 ASP cc_start: 0.8038 (t0) cc_final: 0.7515 (t0) REVERT: B 894 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8791 (tp) REVERT: C 102 ARG cc_start: 0.5884 (mmp-170) cc_final: 0.5401 (ttm170) REVERT: C 133 PHE cc_start: 0.7939 (m-80) cc_final: 0.7603 (m-80) REVERT: C 367 TYR cc_start: 0.8716 (t80) cc_final: 0.8127 (t80) REVERT: C 368 ASN cc_start: 0.8174 (m-40) cc_final: 0.7817 (p0) REVERT: C 423 LEU cc_start: 0.8009 (mm) cc_final: 0.7733 (mm) REVERT: C 450 ARG cc_start: 0.7308 (mtm180) cc_final: 0.6987 (ptm160) REVERT: C 513 PHE cc_start: 0.7617 (m-80) cc_final: 0.7318 (m-80) REVERT: C 584 ASP cc_start: 0.8489 (t0) cc_final: 0.8135 (m-30) REVERT: C 1038 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8800 (m) REVERT: F 123 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7887 (ppp) REVERT: F 270 MET cc_start: 0.5544 (mmm) cc_final: 0.5303 (mmm) REVERT: F 366 MET cc_start: 0.4023 (mmp) cc_final: 0.3538 (mpp) REVERT: G 26 LYS cc_start: 0.6462 (mttt) cc_final: 0.6077 (tppt) REVERT: G 152 MET cc_start: -0.0703 (ptt) cc_final: -0.0908 (mtp) REVERT: G 227 GLU cc_start: 0.4559 (pm20) cc_final: 0.4172 (pp20) REVERT: G 249 MET cc_start: 0.1492 (mpt) cc_final: 0.1258 (mpt) REVERT: G 323 MET cc_start: 0.2331 (tpp) cc_final: 0.2078 (tpp) REVERT: G 360 MET cc_start: 0.1250 (tpp) cc_final: 0.0062 (ptm) REVERT: G 573 VAL cc_start: 0.1459 (t) cc_final: 0.0510 (p) REVERT: H 123 MET cc_start: 0.3889 (ppp) cc_final: 0.3375 (pmm) REVERT: H 323 MET cc_start: 0.4394 (tmm) cc_final: 0.3444 (ppp) REVERT: H 366 MET cc_start: 0.3984 (tpt) cc_final: 0.3533 (OUTLIER) REVERT: H 462 MET cc_start: 0.7557 (ptp) cc_final: 0.7160 (mmt) REVERT: H 474 MET cc_start: 0.1842 (ppp) cc_final: 0.0956 (ppp) REVERT: H 557 MET cc_start: 0.7599 (ppp) cc_final: 0.6905 (ppp) REVERT: H 572 ASN cc_start: 0.6797 (m-40) cc_final: 0.6313 (p0) outliers start: 80 outliers final: 45 residues processed: 253 average time/residue: 0.6389 time to fit residues: 202.7162 Evaluate side-chains 225 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1131 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 367 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 148 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 301 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 chunk 421 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN C 448 ASN C1003 GLN F 117 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.182155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.116894 restraints weight = 76768.819| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.42 r_work: 0.3076 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 41136 Z= 0.138 Angle : 0.606 17.363 56137 Z= 0.295 Chirality : 0.044 0.267 6437 Planarity : 0.004 0.057 7087 Dihedral : 6.723 73.986 7323 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer: Outliers : 1.97 % Allowed : 14.00 % Favored : 84.04 % 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: 0.16 (0.12), residues: 4815 helix: 1.71 (0.13), residues: 1705 sheet: 0.49 (0.19), residues: 702 loop : -1.24 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1037 TYR 0.022 0.001 TYR H 385 PHE 0.031 0.001 PHE F 369 TRP 0.012 0.001 TRP A 434 HIS 0.005 0.001 HIS F 373 Details of bonding type rmsd covalent geometry : bond 0.00326 (40988) covalent geometry : angle 0.58496 (55741) SS BOND : bond 0.00348 ( 48) SS BOND : angle 1.66238 ( 96) hydrogen bonds : bond 0.05039 ( 1737) hydrogen bonds : angle 4.56586 ( 4869) link_BETA1-4 : bond 0.00392 ( 43) link_BETA1-4 : angle 2.00773 ( 129) link_NAG-ASN : bond 0.00265 ( 57) link_NAG-ASN : angle 2.06666 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 193 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8792 (m-30) cc_final: 0.8556 (t0) REVERT: A 322 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: A 572 ASP cc_start: 0.8292 (m-30) cc_final: 0.7898 (m-30) REVERT: A 876 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 986 GLU cc_start: 0.8880 (mp0) cc_final: 0.8445 (mp0) REVERT: B 114 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7735 (p) REVERT: B 499 ASN cc_start: 0.2549 (OUTLIER) cc_final: 0.2068 (p0) REVERT: B 572 ASP cc_start: 0.7642 (m-30) cc_final: 0.6914 (m-30) REVERT: C 133 PHE cc_start: 0.8017 (m-80) cc_final: 0.7630 (m-80) REVERT: C 171 GLN cc_start: 0.8717 (mp10) cc_final: 0.7861 (tm130) REVERT: C 367 TYR cc_start: 0.8740 (t80) cc_final: 0.8141 (t80) REVERT: C 368 ASN cc_start: 0.8223 (m-40) cc_final: 0.7852 (p0) REVERT: C 375 PHE cc_start: 0.8125 (t80) cc_final: 0.7823 (t80) REVERT: C 423 LEU cc_start: 0.7971 (mm) cc_final: 0.7753 (mm) REVERT: C 450 ARG cc_start: 0.7254 (mtm180) cc_final: 0.6951 (ptm160) REVERT: F 123 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7915 (ppp) REVERT: F 366 MET cc_start: 0.4133 (mmp) cc_final: 0.3929 (mpp) REVERT: F 527 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8195 (tt0) REVERT: G 26 LYS cc_start: 0.6464 (mttt) cc_final: 0.6066 (tppt) REVERT: G 152 MET cc_start: -0.0629 (ptt) cc_final: -0.0841 (mtp) REVERT: G 227 GLU cc_start: 0.4555 (pm20) cc_final: 0.4153 (pp20) REVERT: G 323 MET cc_start: 0.1900 (tpp) cc_final: 0.1596 (tpp) REVERT: G 360 MET cc_start: 0.1328 (tpp) cc_final: 0.0165 (ptp) REVERT: H 323 MET cc_start: 0.4539 (tmm) cc_final: 0.3563 (ppp) REVERT: H 366 MET cc_start: 0.4034 (tpt) cc_final: 0.3680 (OUTLIER) REVERT: H 462 MET cc_start: 0.7600 (ptp) cc_final: 0.7173 (mmt) REVERT: H 474 MET cc_start: 0.1697 (ppp) cc_final: 0.0767 (ppp) REVERT: H 557 MET cc_start: 0.7560 (ppp) cc_final: 0.6822 (ppp) REVERT: H 572 ASN cc_start: 0.6875 (m-40) cc_final: 0.6401 (p0) REVERT: H 579 MET cc_start: 0.3353 (mmt) cc_final: 0.2418 (tpp) outliers start: 84 outliers final: 41 residues processed: 261 average time/residue: 0.6146 time to fit residues: 202.6044 Evaluate side-chains 221 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 471 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 174 optimal weight: 0.7980 chunk 442 optimal weight: 30.0000 chunk 385 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 417 optimal weight: 50.0000 chunk 271 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 0.0060 chunk 464 optimal weight: 0.0970 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN C1003 GLN F 194 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.181670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.116526 restraints weight = 76888.178| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.33 r_work: 0.3065 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 41136 Z= 0.166 Angle : 0.621 17.884 56137 Z= 0.302 Chirality : 0.045 0.261 6437 Planarity : 0.004 0.062 7087 Dihedral : 6.557 70.206 7323 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.37 % Rotamer: Outliers : 2.32 % Allowed : 14.65 % Favored : 83.03 % 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: 0.16 (0.12), residues: 4815 helix: 1.72 (0.13), residues: 1705 sheet: 0.49 (0.19), residues: 702 loop : -1.26 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1037 TYR 0.022 0.001 TYR C1065 PHE 0.028 0.001 PHE F 369 TRP 0.013 0.001 TRP H 477 HIS 0.015 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00405 (40988) covalent geometry : angle 0.60021 (55741) SS BOND : bond 0.00360 ( 48) SS BOND : angle 1.71258 ( 96) hydrogen bonds : bond 0.05285 ( 1737) hydrogen bonds : angle 4.56041 ( 4869) link_BETA1-4 : bond 0.00368 ( 43) link_BETA1-4 : angle 2.05116 ( 129) link_NAG-ASN : bond 0.00258 ( 57) link_NAG-ASN : angle 2.10698 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 183 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8791 (m-30) cc_final: 0.8551 (t0) REVERT: A 322 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7976 (pt0) REVERT: A 572 ASP cc_start: 0.8336 (m-30) cc_final: 0.7978 (m-30) REVERT: A 876 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8868 (tt) REVERT: A 986 GLU cc_start: 0.8847 (mp0) cc_final: 0.8456 (mp0) REVERT: B 114 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7712 (p) REVERT: B 499 ASN cc_start: 0.2765 (OUTLIER) cc_final: 0.2236 (p0) REVERT: B 572 ASP cc_start: 0.7677 (m-30) cc_final: 0.6937 (m-30) REVERT: C 102 ARG cc_start: 0.5871 (mmp-170) cc_final: 0.5464 (ttm170) REVERT: C 133 PHE cc_start: 0.8109 (m-80) cc_final: 0.7721 (m-80) REVERT: C 171 GLN cc_start: 0.8723 (mp10) cc_final: 0.7771 (tm130) REVERT: C 367 TYR cc_start: 0.8661 (t80) cc_final: 0.8155 (t80) REVERT: C 368 ASN cc_start: 0.8229 (m-40) cc_final: 0.7839 (p0) REVERT: C 375 PHE cc_start: 0.8302 (t80) cc_final: 0.8057 (t80) REVERT: C 450 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6971 (ptm160) REVERT: C 584 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: C 1038 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8853 (m) REVERT: F 123 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7879 (ppp) REVERT: F 152 MET cc_start: 0.3436 (ppp) cc_final: 0.2515 (ttp) REVERT: F 176 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7182 (tp) REVERT: G 26 LYS cc_start: 0.6463 (mttt) cc_final: 0.6008 (tppt) REVERT: G 152 MET cc_start: -0.0710 (ptt) cc_final: -0.1023 (mtp) REVERT: G 227 GLU cc_start: 0.4614 (pm20) cc_final: 0.4230 (pp20) REVERT: G 249 MET cc_start: 0.1401 (mpt) cc_final: 0.1187 (mpt) REVERT: G 323 MET cc_start: 0.1921 (tpp) cc_final: 0.1613 (tpp) REVERT: G 360 MET cc_start: 0.1291 (tpp) cc_final: 0.0181 (ptp) REVERT: H 123 MET cc_start: 0.3981 (ppp) cc_final: 0.3389 (pmm) REVERT: H 297 MET cc_start: 0.2278 (pmm) cc_final: 0.1985 (pmm) REVERT: H 323 MET cc_start: 0.4442 (tmm) cc_final: 0.3491 (ppp) REVERT: H 332 MET cc_start: 0.3907 (pp-130) cc_final: 0.1168 (ptm) REVERT: H 366 MET cc_start: 0.4202 (tpt) cc_final: 0.3732 (OUTLIER) REVERT: H 462 MET cc_start: 0.7577 (ptp) cc_final: 0.7196 (mmt) REVERT: H 474 MET cc_start: 0.1774 (ppp) cc_final: 0.0916 (ppp) REVERT: H 557 MET cc_start: 0.7602 (ppp) cc_final: 0.6896 (ppp) REVERT: H 572 ASN cc_start: 0.6824 (m-40) cc_final: 0.6388 (p0) REVERT: H 579 MET cc_start: 0.3472 (mmt) cc_final: 0.2656 (tpp) outliers start: 99 outliers final: 54 residues processed: 262 average time/residue: 0.5968 time to fit residues: 198.2036 Evaluate side-chains 238 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain G residue 239 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 285 optimal weight: 2.9990 chunk 367 optimal weight: 40.0000 chunk 428 optimal weight: 30.0000 chunk 408 optimal weight: 40.0000 chunk 295 optimal weight: 0.9980 chunk 318 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 473 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 449 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 912 ASN C1003 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** 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 = 0.4548 r_free = 0.4548 target = 0.181334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.119333 restraints weight = 76661.918| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 4.56 r_work: 0.3041 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 41136 Z= 0.186 Angle : 0.632 18.107 56137 Z= 0.308 Chirality : 0.045 0.267 6437 Planarity : 0.004 0.059 7087 Dihedral : 6.473 65.986 7323 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.48 % Favored : 94.50 % Rotamer: Outliers : 2.34 % Allowed : 15.47 % Favored : 82.19 % 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: 0.13 (0.12), residues: 4815 helix: 1.71 (0.13), residues: 1705 sheet: 0.47 (0.19), residues: 714 loop : -1.29 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1037 TYR 0.022 0.001 TYR C1065 PHE 0.029 0.002 PHE F 369 TRP 0.012 0.001 TRP H 477 HIS 0.016 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00459 (40988) covalent geometry : angle 0.61106 (55741) SS BOND : bond 0.00382 ( 48) SS BOND : angle 1.68471 ( 96) hydrogen bonds : bond 0.05504 ( 1737) hydrogen bonds : angle 4.58766 ( 4869) link_BETA1-4 : bond 0.00368 ( 43) link_BETA1-4 : angle 2.09244 ( 129) link_NAG-ASN : bond 0.00263 ( 57) link_NAG-ASN : angle 2.13853 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 179 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 196 ASP cc_start: 0.8824 (m-30) cc_final: 0.8552 (t0) REVERT: A 322 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: A 572 ASP cc_start: 0.8341 (m-30) cc_final: 0.7970 (m-30) REVERT: A 876 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8846 (tt) REVERT: A 986 GLU cc_start: 0.8870 (mp0) cc_final: 0.8535 (mp0) REVERT: B 114 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7789 (p) REVERT: B 499 ASN cc_start: 0.2755 (OUTLIER) cc_final: 0.2228 (p0) REVERT: B 572 ASP cc_start: 0.7668 (m-30) cc_final: 0.6925 (m-30) REVERT: B 1011 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8694 (mm) REVERT: C 102 ARG cc_start: 0.5806 (mmp-170) cc_final: 0.5447 (ttm170) REVERT: C 133 PHE cc_start: 0.7992 (m-80) cc_final: 0.7575 (m-80) REVERT: C 171 GLN cc_start: 0.8753 (mp10) cc_final: 0.7740 (tm130) REVERT: C 367 TYR cc_start: 0.8685 (t80) cc_final: 0.8192 (t80) REVERT: C 368 ASN cc_start: 0.8239 (m-40) cc_final: 0.7839 (p0) REVERT: C 375 PHE cc_start: 0.8304 (t80) cc_final: 0.8091 (t80) REVERT: C 450 ARG cc_start: 0.7262 (mtm180) cc_final: 0.6953 (ptm160) REVERT: C 584 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: C 1011 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8656 (mm) REVERT: C 1038 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8846 (m) REVERT: F 152 MET cc_start: 0.3401 (ppp) cc_final: 0.2426 (ttp) REVERT: F 176 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7239 (tp) REVERT: F 366 MET cc_start: 0.4776 (mmp) cc_final: 0.4556 (mpp) REVERT: F 455 MET cc_start: 0.8033 (tmm) cc_final: 0.7734 (tmm) REVERT: G 26 LYS cc_start: 0.6525 (mttt) cc_final: 0.6057 (tppt) REVERT: G 152 MET cc_start: -0.0637 (ptt) cc_final: -0.0895 (mtp) REVERT: G 227 GLU cc_start: 0.4589 (pm20) cc_final: 0.4220 (pp20) REVERT: G 360 MET cc_start: 0.1328 (tpp) cc_final: 0.0203 (ptm) REVERT: H 297 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.2021 (pmm) REVERT: H 323 MET cc_start: 0.4400 (tmm) cc_final: 0.3498 (ppp) REVERT: H 332 MET cc_start: 0.4066 (pp-130) cc_final: 0.1318 (ptm) REVERT: H 366 MET cc_start: 0.4224 (tpt) cc_final: 0.3772 (OUTLIER) REVERT: H 462 MET cc_start: 0.7574 (ptp) cc_final: 0.7167 (mmt) REVERT: H 474 MET cc_start: 0.1843 (ppp) cc_final: 0.0966 (ppp) REVERT: H 557 MET cc_start: 0.7593 (ppp) cc_final: 0.7262 (ttt) REVERT: H 572 ASN cc_start: 0.6895 (m-40) cc_final: 0.6509 (p0) outliers start: 100 outliers final: 66 residues processed: 260 average time/residue: 0.6077 time to fit residues: 200.6488 Evaluate side-chains 249 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 297 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 224 optimal weight: 3.9990 chunk 466 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 423 optimal weight: 30.0000 chunk 397 optimal weight: 20.0000 chunk 474 optimal weight: 20.0000 chunk 389 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 499 ASN C1003 GLN F 330 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 HIS ** 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 = 0.4535 r_free = 0.4535 target = 0.180253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.114441 restraints weight = 76724.484| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.91 r_work: 0.3004 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 41136 Z= 0.271 Angle : 0.697 18.803 56137 Z= 0.341 Chirality : 0.048 0.273 6437 Planarity : 0.005 0.059 7087 Dihedral : 6.634 63.737 7323 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 2.53 % Allowed : 15.89 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 4815 helix: 1.58 (0.12), residues: 1705 sheet: 0.42 (0.19), residues: 699 loop : -1.38 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1037 TYR 0.025 0.002 TYR C1065 PHE 0.026 0.002 PHE F 369 TRP 0.012 0.001 TRP H 477 HIS 0.008 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00678 (40988) covalent geometry : angle 0.67510 (55741) SS BOND : bond 0.00483 ( 48) SS BOND : angle 1.90318 ( 96) hydrogen bonds : bond 0.06341 ( 1737) hydrogen bonds : angle 4.72069 ( 4869) link_BETA1-4 : bond 0.00357 ( 43) link_BETA1-4 : angle 2.23173 ( 129) link_NAG-ASN : bond 0.00333 ( 57) link_NAG-ASN : angle 2.28414 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 178 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: A 196 ASP cc_start: 0.8815 (m-30) cc_final: 0.8555 (t0) REVERT: A 876 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8827 (tt) REVERT: A 986 GLU cc_start: 0.8902 (mp0) cc_final: 0.8519 (mp0) REVERT: B 114 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7691 (p) REVERT: B 499 ASN cc_start: 0.2806 (OUTLIER) cc_final: 0.2406 (p0) REVERT: B 572 ASP cc_start: 0.7697 (m-30) cc_final: 0.6976 (m-30) REVERT: B 584 ASP cc_start: 0.8045 (t0) cc_final: 0.7499 (t0) REVERT: C 102 ARG cc_start: 0.6046 (mmp-170) cc_final: 0.5542 (ttm170) REVERT: C 133 PHE cc_start: 0.7944 (m-80) cc_final: 0.7529 (m-80) REVERT: C 171 GLN cc_start: 0.8765 (mp10) cc_final: 0.7740 (tm130) REVERT: C 367 TYR cc_start: 0.8699 (t80) cc_final: 0.8198 (t80) REVERT: C 368 ASN cc_start: 0.8263 (m-40) cc_final: 0.7852 (p0) REVERT: C 375 PHE cc_start: 0.8373 (t80) cc_final: 0.8138 (t80) REVERT: C 584 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: C 1011 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8735 (mm) REVERT: C 1038 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8861 (m) REVERT: F 152 MET cc_start: 0.3199 (ppp) cc_final: 0.2392 (ttp) REVERT: F 176 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7181 (tp) REVERT: F 455 MET cc_start: 0.8008 (tmm) cc_final: 0.7739 (tmm) REVERT: G 26 LYS cc_start: 0.6396 (mttt) cc_final: 0.5949 (tppt) REVERT: G 152 MET cc_start: -0.0827 (ptt) cc_final: -0.1125 (mtp) REVERT: G 227 GLU cc_start: 0.4666 (pm20) cc_final: 0.4308 (pp20) REVERT: G 360 MET cc_start: 0.1290 (tpp) cc_final: 0.0123 (ptp) REVERT: H 123 MET cc_start: 0.4067 (ppp) cc_final: 0.3763 (pmm) REVERT: H 297 MET cc_start: 0.2353 (OUTLIER) cc_final: 0.2066 (pmm) REVERT: H 323 MET cc_start: 0.4204 (tmm) cc_final: 0.3317 (ppp) REVERT: H 366 MET cc_start: 0.4271 (tpt) cc_final: 0.3833 (OUTLIER) REVERT: H 462 MET cc_start: 0.7545 (ptp) cc_final: 0.7157 (mmt) REVERT: H 474 MET cc_start: 0.1992 (ppp) cc_final: 0.1088 (ppp) REVERT: H 557 MET cc_start: 0.7591 (ppp) cc_final: 0.7242 (ttt) REVERT: H 572 ASN cc_start: 0.6931 (m-40) cc_final: 0.6543 (p0) outliers start: 108 outliers final: 67 residues processed: 271 average time/residue: 0.6203 time to fit residues: 211.9811 Evaluate side-chains 249 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 23 optimal weight: 0.0170 chunk 136 optimal weight: 0.1980 chunk 330 optimal weight: 5.9990 chunk 294 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 471 optimal weight: 6.9990 chunk 434 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN C1003 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.182370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.117331 restraints weight = 76785.654| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 4.23 r_work: 0.3094 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 41136 Z= 0.122 Angle : 0.605 17.728 56137 Z= 0.292 Chirality : 0.044 0.273 6437 Planarity : 0.004 0.059 7087 Dihedral : 6.156 59.255 7323 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 1.57 % Allowed : 16.90 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 4815 helix: 1.75 (0.13), residues: 1706 sheet: 0.51 (0.19), residues: 690 loop : -1.27 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.022 0.001 TYR H 385 PHE 0.030 0.001 PHE F 369 TRP 0.024 0.001 TRP G 478 HIS 0.005 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00280 (40988) covalent geometry : angle 0.58495 (55741) SS BOND : bond 0.00295 ( 48) SS BOND : angle 1.37622 ( 96) hydrogen bonds : bond 0.04643 ( 1737) hydrogen bonds : angle 4.50369 ( 4869) link_BETA1-4 : bond 0.00401 ( 43) link_BETA1-4 : angle 2.09378 ( 129) link_NAG-ASN : bond 0.00286 ( 57) link_NAG-ASN : angle 2.03528 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 1.515 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 196 ASP cc_start: 0.8847 (m-30) cc_final: 0.8629 (t0) REVERT: A 572 ASP cc_start: 0.8261 (m-30) cc_final: 0.7904 (m-30) REVERT: A 771 GLU cc_start: 0.8486 (tt0) cc_final: 0.7864 (tt0) REVERT: A 876 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8824 (tt) REVERT: A 986 GLU cc_start: 0.8700 (mp0) cc_final: 0.8443 (mp0) REVERT: A 1111 GLN cc_start: 0.8879 (mt0) cc_final: 0.8438 (mt0) REVERT: B 114 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7736 (p) REVERT: B 499 ASN cc_start: 0.2701 (OUTLIER) cc_final: 0.2253 (p0) REVERT: B 572 ASP cc_start: 0.7656 (m-30) cc_final: 0.6897 (m-30) REVERT: C 133 PHE cc_start: 0.8017 (m-80) cc_final: 0.7588 (m-80) REVERT: C 367 TYR cc_start: 0.8719 (t80) cc_final: 0.8199 (t80) REVERT: C 368 ASN cc_start: 0.8261 (m-40) cc_final: 0.7832 (p0) REVERT: C 584 ASP cc_start: 0.8477 (t0) cc_final: 0.8077 (m-30) REVERT: F 152 MET cc_start: 0.3045 (ppp) cc_final: 0.2336 (ttp) REVERT: F 176 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7195 (tp) REVERT: F 249 MET cc_start: 0.3972 (mmt) cc_final: 0.3662 (mpp) REVERT: F 323 MET cc_start: 0.6950 (tmm) cc_final: 0.6557 (tpp) REVERT: G 26 LYS cc_start: 0.6525 (mttt) cc_final: 0.6062 (tppt) REVERT: G 152 MET cc_start: -0.0754 (ptt) cc_final: -0.1057 (mtp) REVERT: G 227 GLU cc_start: 0.4591 (pm20) cc_final: 0.4248 (pp20) REVERT: G 360 MET cc_start: 0.1618 (tpp) cc_final: 0.0427 (ptp) REVERT: G 480 MET cc_start: 0.2163 (pp-130) cc_final: 0.1472 (mtp) REVERT: H 297 MET cc_start: 0.2278 (OUTLIER) cc_final: 0.1999 (pmm) REVERT: H 323 MET cc_start: 0.4362 (tmm) cc_final: 0.3472 (ppp) REVERT: H 332 MET cc_start: 0.3877 (pp-130) cc_final: 0.1720 (ptm) REVERT: H 366 MET cc_start: 0.4233 (tpt) cc_final: 0.3787 (OUTLIER) REVERT: H 462 MET cc_start: 0.7553 (ptp) cc_final: 0.7158 (mmt) REVERT: H 474 MET cc_start: 0.0938 (ppp) cc_final: 0.0182 (ppp) REVERT: H 557 MET cc_start: 0.7591 (ppp) cc_final: 0.7249 (ttt) REVERT: H 572 ASN cc_start: 0.6964 (m-40) cc_final: 0.6578 (p0) REVERT: H 579 MET cc_start: 0.3491 (mmt) cc_final: 0.2558 (tpp) outliers start: 67 outliers final: 48 residues processed: 246 average time/residue: 0.6350 time to fit residues: 196.1218 Evaluate side-chains 221 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 34 optimal weight: 0.2980 chunk 241 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 276 optimal weight: 0.0020 chunk 16 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 362 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 499 ASN B 899 GLN C 912 ASN C1003 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.183558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.116758 restraints weight = 76444.063| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 5.14 r_work: 0.3085 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 41136 Z= 0.111 Angle : 0.611 17.276 56137 Z= 0.292 Chirality : 0.043 0.261 6437 Planarity : 0.004 0.059 7087 Dihedral : 5.936 56.120 7323 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer: Outliers : 1.31 % Allowed : 17.32 % Favored : 81.37 % 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: 0.28 (0.12), residues: 4815 helix: 1.78 (0.13), residues: 1706 sheet: 0.65 (0.19), residues: 725 loop : -1.22 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 406 TYR 0.023 0.001 TYR G 237 PHE 0.033 0.001 PHE A 757 TRP 0.017 0.001 TRP G 478 HIS 0.014 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00245 (40988) covalent geometry : angle 0.59201 (55741) SS BOND : bond 0.00274 ( 48) SS BOND : angle 1.31390 ( 96) hydrogen bonds : bond 0.04278 ( 1737) hydrogen bonds : angle 4.42402 ( 4869) link_BETA1-4 : bond 0.00408 ( 43) link_BETA1-4 : angle 2.06256 ( 129) link_NAG-ASN : bond 0.00274 ( 57) link_NAG-ASN : angle 1.99939 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 1.729 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 196 ASP cc_start: 0.8847 (m-30) cc_final: 0.8629 (t0) REVERT: A 240 LEU cc_start: 0.7170 (mp) cc_final: 0.6551 (tp) REVERT: A 322 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: A 456 LYS cc_start: 0.8327 (mppt) cc_final: 0.7834 (mptt) REVERT: A 572 ASP cc_start: 0.8266 (m-30) cc_final: 0.7829 (m-30) REVERT: A 750 LEU cc_start: 0.9432 (mp) cc_final: 0.9193 (mp) REVERT: A 771 GLU cc_start: 0.8436 (tt0) cc_final: 0.7803 (tt0) REVERT: A 876 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 986 GLU cc_start: 0.8712 (mp0) cc_final: 0.8474 (mp0) REVERT: A 1111 GLN cc_start: 0.8846 (mt0) cc_final: 0.8442 (mt0) REVERT: B 114 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7693 (p) REVERT: B 499 ASN cc_start: 0.2530 (OUTLIER) cc_final: 0.2106 (p0) REVERT: B 572 ASP cc_start: 0.7664 (m-30) cc_final: 0.6880 (m-30) REVERT: C 133 PHE cc_start: 0.7945 (m-80) cc_final: 0.7566 (m-80) REVERT: C 171 GLN cc_start: 0.8725 (mp10) cc_final: 0.7698 (tm130) REVERT: C 367 TYR cc_start: 0.8695 (t80) cc_final: 0.8188 (t80) REVERT: C 368 ASN cc_start: 0.8256 (m-40) cc_final: 0.7826 (p0) REVERT: C 584 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: F 152 MET cc_start: 0.3030 (ppp) cc_final: 0.2302 (ttp) REVERT: F 176 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7213 (tp) REVERT: F 249 MET cc_start: 0.3973 (mmt) cc_final: 0.3668 (mpp) REVERT: F 323 MET cc_start: 0.6904 (tmm) cc_final: 0.6475 (tpp) REVERT: G 26 LYS cc_start: 0.6525 (mttt) cc_final: 0.6083 (tppt) REVERT: G 152 MET cc_start: -0.0860 (ptt) cc_final: -0.1149 (mtp) REVERT: G 227 GLU cc_start: 0.4767 (pm20) cc_final: 0.4416 (pp20) REVERT: G 360 MET cc_start: 0.1611 (tpp) cc_final: 0.0493 (ptm) REVERT: G 480 MET cc_start: 0.2288 (pp-130) cc_final: 0.1697 (mtp) REVERT: H 297 MET cc_start: 0.2267 (OUTLIER) cc_final: 0.1989 (pmm) REVERT: H 323 MET cc_start: 0.4158 (tmm) cc_final: 0.3281 (ppp) REVERT: H 332 MET cc_start: 0.3874 (pp-130) cc_final: 0.1703 (ptm) REVERT: H 366 MET cc_start: 0.4218 (tpt) cc_final: 0.3774 (OUTLIER) REVERT: H 462 MET cc_start: 0.7566 (ptp) cc_final: 0.7190 (mmt) REVERT: H 474 MET cc_start: 0.0941 (ppp) cc_final: 0.0170 (ppp) REVERT: H 557 MET cc_start: 0.7573 (ppp) cc_final: 0.7227 (ttt) REVERT: H 572 ASN cc_start: 0.6986 (m-40) cc_final: 0.6614 (p0) REVERT: H 579 MET cc_start: 0.3542 (mmt) cc_final: 0.2572 (tpp) outliers start: 56 outliers final: 37 residues processed: 231 average time/residue: 0.6379 time to fit residues: 185.3281 Evaluate side-chains 221 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 238 optimal weight: 6.9990 chunk 469 optimal weight: 30.0000 chunk 414 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 473 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 0.0670 chunk 456 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 409 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 499 ASN B 578 GLN B 899 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.181324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.115650 restraints weight = 76944.811| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 4.83 r_work: 0.3033 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 41136 Z= 0.193 Angle : 0.665 18.090 56137 Z= 0.322 Chirality : 0.046 0.314 6437 Planarity : 0.004 0.058 7087 Dihedral : 6.100 58.331 7323 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.41 % Rotamer: Outliers : 1.47 % Allowed : 17.13 % Favored : 81.39 % 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: 0.18 (0.12), residues: 4815 helix: 1.73 (0.13), residues: 1705 sheet: 0.53 (0.19), residues: 724 loop : -1.26 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1037 TYR 0.024 0.001 TYR C1065 PHE 0.039 0.002 PHE A 757 TRP 0.017 0.001 TRP G 478 HIS 0.006 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00478 (40988) covalent geometry : angle 0.64460 (55741) SS BOND : bond 0.00431 ( 48) SS BOND : angle 1.85535 ( 96) hydrogen bonds : bond 0.05472 ( 1737) hydrogen bonds : angle 4.57664 ( 4869) link_BETA1-4 : bond 0.00370 ( 43) link_BETA1-4 : angle 2.12067 ( 129) link_NAG-ASN : bond 0.00269 ( 57) link_NAG-ASN : angle 2.13798 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21044.67 seconds wall clock time: 356 minutes 59.67 seconds (21419.67 seconds total)