Starting phenix.real_space_refine on Sun Feb 8 03:19:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8a_31795/02_2026/7v8a_31795.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8a_31795/02_2026/7v8a_31795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v8a_31795/02_2026/7v8a_31795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8a_31795/02_2026/7v8a_31795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v8a_31795/02_2026/7v8a_31795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8a_31795/02_2026/7v8a_31795.map" } resolution = 2.7 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= 0.067 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 25408 2.51 5 N 6527 2.21 5 O 7792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39922 Number of models: 1 Model: "" Number of chains: 50 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: "A" 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: "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: 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.92, per 1000 atoms: 0.25 Number of scatterers: 39922 At special positions: 0 Unit cell: (165, 174.9, 239.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 7792 8.00 N 6527 7.00 C 25408 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 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=2.02 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " 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 341 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F2001 " - " ASN F 53 " " NAG G2001 " - " ASN G 53 " " NAG G2002 " - " ASN G 322 " " NAG H 901 " - " ASN H 322 " " NAG I 1 " - " ASN A 232 " " NAG J 1 " - " ASN A 280 " " NAG K 1 " - " ASN A 329 " " NAG L 1 " - " ASN A 614 " " NAG M 1 " - " ASN A 707 " " NAG N 1 " - " ASN A 715 " " NAG O 1 " - " ASN A 799 " " NAG P 1 " - " ASN A1072 " " NAG Q 1 " - " ASN A1096 " " NAG R 1 " - " ASN A1132 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 163 " " NAG U 1 " - " ASN B 232 " " NAG V 1 " - " ASN B 280 " " NAG W 1 " - " ASN B 329 " " NAG X 1 " - " ASN B 614 " " NAG Y 1 " - " ASN B 707 " " NAG Z 1 " - " ASN B 715 " " NAG a 1 " - " ASN B 799 " " NAG b 1 " - " ASN B1072 " " NAG c 1 " - " ASN B1096 " " NAG d 1 " - " ASN B1132 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 163 " " NAG g 1 " - " ASN C 232 " " NAG h 1 " - " ASN C 280 " " NAG i 1 " - " ASN C 329 " " NAG j 1 " - " ASN C 614 " " NAG k 1 " - " ASN C 707 " " NAG l 1 " - " ASN C 715 " " NAG m 1 " - " ASN C 799 " " NAG n 1 " - " ASN C1072 " " NAG o 1 " - " ASN C1096 " " NAG p 1 " - " ASN C1132 " " NAG q 1 " - " ASN F 322 " Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.8 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: 150 helices and 52 sheets defined 39.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 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 363 through 368 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.250A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.191A 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 500 through 503 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.954A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 781 removed outlier: 3.576A pdb=" N ALA A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.635A 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 916 removed outlier: 4.078A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 981 removed outlier: 3.667A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.262A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.793A 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: 3.555A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 4.048A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.961A pdb=" N ASN B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.395A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.025A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 781 Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.530A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.656A 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 916 removed outlier: 4.022A pdb=" N LEU B 914 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.756A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 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 980 Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.768A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.146A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.456A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 742 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.180A 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 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.588A 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: 3.993A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.744A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 974 through 981 removed outlier: 4.077A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 3.860A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.970A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 79 removed outlier: 3.514A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.710A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.649A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.862A 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 174 Processing helix chain 'F' and resid 176 through 194 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: 3.534A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (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 265 through 268 removed outlier: 4.092A pdb=" N GLY F 268 " --> pdb=" O HIS F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.792A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.400A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.807A 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: 3.989A 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 485 removed outlier: 3.726A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.638A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.693A 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: 4.069A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.598A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) 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 597 removed outlier: 3.875A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.526A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 79 removed outlier: 4.152A pdb=" N ASN G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.565A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 removed outlier: 3.817A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.798A pdb=" N LEU G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 194 Processing helix chain 'G' and resid 198 through 205 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: 3.818A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 250 Processing helix chain 'G' and resid 293 through 300 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 removed outlier: 3.909A pdb=" N ARG G 393 " --> pdb=" O PHE G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 412 removed outlier: 4.154A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.265A 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 446 removed outlier: 3.830A 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: 3.548A pdb=" N ARG G 482 " --> pdb=" O TRP G 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 508 removed outlier: 4.219A pdb=" N SER G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN G 508 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 508' Processing helix chain 'G' and resid 512 through 532 removed outlier: 4.078A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 519 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU G 520 " --> pdb=" O TYR G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 4.038A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 4.207A 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 removed outlier: 3.599A pdb=" N PHE G 588 " --> pdb=" O LEU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.595A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.519A pdb=" N GLN H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 80 removed outlier: 3.742A pdb=" N MET H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 4.085A pdb=" N SER H 106 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 108' Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 159 through 172 removed outlier: 3.560A pdb=" N VAL H 172 " --> pdb=" O TRP H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.353A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 removed outlier: 3.607A pdb=" N TYR H 202 " --> pdb=" O ASP H 198 " (cutoff:3.500A) 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: 3.638A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.206A 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 removed outlier: 3.547A pdb=" N MET H 249 " --> pdb=" O ARG H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.193A pdb=" N SER H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 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 385 Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.773A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 412 removed outlier: 4.109A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.876A 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: 3.789A 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: 3.509A pdb=" N TRP H 477 " --> pdb=" O TRP H 473 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG H 482 " --> pdb=" O TRP H 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU H 483 " --> pdb=" O GLU H 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.911A pdb=" N SER H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 532 removed outlier: 4.304A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.586A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 removed outlier: 3.978A pdb=" N SER H 563 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 3.773A 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 Processing helix chain 'H' and resid 588 through 599 removed outlier: 3.980A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.958A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.912A 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: 5.951A pdb=" N PHE A 43 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.056A 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: 7.196A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.554A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.467A 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: 5.865A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.025A 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: 6.808A 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: 6.359A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.171A 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 701 removed outlier: 6.716A 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 removed outlier: 3.722A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 6.038A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.842A 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: 4.531A 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 787 removed outlier: 3.503A pdb=" N ASN C 701 " --> pdb=" O ILE A 786 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.167A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.566A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 324 removed outlier: 5.740A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.711A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 658 removed outlier: 6.007A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N VAL B 654 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.927A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 709 through 711 removed outlier: 3.684A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 726 removed outlier: 3.541A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.496A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.879A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.063A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.191A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N VAL C 126 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N GLU C 167 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N ILE C 128 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR C 165 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 130 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU C 132 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 161 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN C 134 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.047A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.632A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.032A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.602A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.531A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.413A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF1, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.745A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'G' and resid 132 through 134 removed outlier: 4.097A pdb=" N ASN G 134 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU G 140 " --> pdb=" O ASN G 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AF6, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.303A pdb=" N ASN H 134 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU H 140 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 350 1709 hydrogen bonds defined for protein. 4830 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: 9.68 Time building geometry restraints manager: 4.89 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: 12682 1.34 - 1.46: 9956 1.46 - 1.58: 17956 1.58 - 1.70: 0 1.70 - 1.82: 282 Bond restraints: 40876 Sorted by residual: bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.87e+00 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 6.53e+00 bond pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 ... (remaining 40871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 54504 1.88 - 3.76: 977 3.76 - 5.65: 82 5.65 - 7.53: 22 7.53 - 9.41: 4 Bond angle restraints: 55589 Sorted by residual: angle pdb=" N VAL H 506 " pdb=" CA VAL H 506 " pdb=" C VAL H 506 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL H 172 " pdb=" CA VAL H 172 " pdb=" C VAL H 172 " ideal model delta sigma weight residual 113.53 108.42 5.11 9.80e-01 1.04e+00 2.71e+01 angle pdb=" N VAL B 157 " pdb=" CA VAL B 157 " pdb=" C VAL B 157 " ideal model delta sigma weight residual 113.42 108.42 5.00 1.17e+00 7.31e-01 1.82e+01 angle pdb=" N ILE A 803 " pdb=" CA ILE A 803 " pdb=" C ILE A 803 " ideal model delta sigma weight residual 113.53 110.00 3.53 9.80e-01 1.04e+00 1.30e+01 angle pdb=" CB ARG G 192 " pdb=" CG ARG G 192 " pdb=" CD ARG G 192 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.87e+00 ... (remaining 55584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.01: 23438 21.01 - 42.02: 1702 42.02 - 63.03: 261 63.03 - 84.04: 61 84.04 - 105.05: 29 Dihedral angle restraints: 25491 sinusoidal: 11274 harmonic: 14217 Sorted by residual: 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 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS B1080 " pdb=" SG CYS B1080 " pdb=" SG CYS B1124 " pdb=" CB CYS B1124 " ideal model delta sinusoidal sigma weight residual -86.00 -0.23 -85.77 1 1.00e+01 1.00e-02 8.89e+01 ... (remaining 25488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5594 0.069 - 0.138: 767 0.138 - 0.207: 31 0.207 - 0.277: 3 0.277 - 0.346: 1 Chirality restraints: 6396 Sorted by residual: chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN C 232 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C4 NAG n 1 " pdb=" C3 NAG n 1 " pdb=" C5 NAG n 1 " pdb=" O4 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 707 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6393 not shown) Planarity restraints: 7132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 232 " 0.024 2.00e-02 2.50e+03 2.18e-02 5.91e+00 pdb=" CG ASN C 232 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 232 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 232 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.019 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN A 232 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 884 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.30e+00 pdb=" CG TRP C 884 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 884 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 884 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 884 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 884 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 884 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 884 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 884 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 884 " 0.002 2.00e-02 2.50e+03 ... (remaining 7129 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 856 2.68 - 3.23: 39140 3.23 - 3.79: 63104 3.79 - 4.34: 81585 4.34 - 4.90: 135190 Nonbonded interactions: 319875 Sorted by model distance: nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.142 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP H 382 " pdb=" OH TYR H 385 " model vdw 2.163 3.040 nonbonded pdb=" OD1 ASP B 566 " pdb=" OG1 THR B 570 " model vdw 2.180 3.040 ... (remaining 319870 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' 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' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 19 through 2001) selection = chain 'H' } 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 39.490 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 41015 Z= 0.195 Angle : 0.601 9.410 55958 Z= 0.293 Chirality : 0.045 0.346 6396 Planarity : 0.004 0.065 7079 Dihedral : 14.605 105.053 16191 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 4815 helix: 1.64 (0.13), residues: 1657 sheet: 0.30 (0.19), residues: 725 loop : -1.36 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 192 TYR 0.015 0.001 TYR A1065 PHE 0.024 0.001 PHE B 904 TRP 0.030 0.001 TRP C 884 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00430 (40876) covalent geometry : angle 0.57850 (55589) SS BOND : bond 0.00336 ( 48) SS BOND : angle 1.38989 ( 96) hydrogen bonds : bond 0.13991 ( 1709) hydrogen bonds : angle 5.73499 ( 4830) link_BETA1-4 : bond 0.00345 ( 38) link_BETA1-4 : angle 2.34009 ( 114) link_NAG-ASN : bond 0.00244 ( 53) link_NAG-ASN : angle 2.23815 ( 159) *********************** 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 397 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8428 (m-80) cc_final: 0.8049 (m-80) REVERT: A 235 ARG cc_start: 0.7302 (mtp180) cc_final: 0.7037 (mtm180) REVERT: B 81 ASN cc_start: 0.7093 (m-40) cc_final: 0.6734 (p0) REVERT: C 186 ASN cc_start: 0.6936 (m-40) cc_final: 0.5930 (p0) REVERT: F 123 MET cc_start: 0.0104 (ptp) cc_final: -0.0912 (ttm) REVERT: F 143 LEU cc_start: 0.5209 (mp) cc_final: 0.5007 (pt) REVERT: F 462 MET cc_start: 0.3215 (mpp) cc_final: 0.2883 (mmp) REVERT: F 510 TYR cc_start: 0.5873 (m-80) cc_final: 0.5587 (m-10) REVERT: F 579 MET cc_start: 0.0086 (mtp) cc_final: -0.1025 (mpp) REVERT: G 56 GLU cc_start: 0.6386 (pm20) cc_final: 0.6148 (pm20) REVERT: G 82 MET cc_start: 0.0266 (pmm) cc_final: -0.0207 (ttp) REVERT: G 95 LEU cc_start: 0.3786 (tt) cc_final: 0.3401 (pp) REVERT: G 123 MET cc_start: 0.0504 (ptt) cc_final: -0.0432 (ttp) REVERT: G 163 TRP cc_start: 0.1920 (t60) cc_final: 0.1563 (t-100) REVERT: G 192 ARG cc_start: 0.3506 (mpp-170) cc_final: 0.3159 (ptp-170) REVERT: G 249 MET cc_start: -0.0214 (mmt) cc_final: -0.1846 (tmm) REVERT: G 297 MET cc_start: -0.0386 (tpp) cc_final: -0.0931 (ttm) REVERT: G 323 MET cc_start: -0.0180 (tpt) cc_final: -0.1036 (tpt) REVERT: G 366 MET cc_start: 0.0568 (mmt) cc_final: 0.0361 (mmt) REVERT: G 376 MET cc_start: 0.2438 (tmm) cc_final: 0.2188 (ttt) REVERT: G 531 GLN cc_start: 0.2949 (mp-120) cc_final: 0.2477 (pt0) REVERT: G 557 MET cc_start: 0.5393 (ppp) cc_final: 0.4996 (tpt) REVERT: H 62 MET cc_start: 0.4373 (mtm) cc_final: 0.4059 (mtt) REVERT: H 94 LYS cc_start: 0.7008 (ttmt) cc_final: 0.6684 (ptmm) REVERT: H 156 LEU cc_start: 0.2301 (tp) cc_final: 0.1975 (mm) REVERT: H 270 MET cc_start: -0.0420 (mtt) cc_final: -0.0782 (mmt) REVERT: H 366 MET cc_start: 0.2526 (tpt) cc_final: 0.1308 (tpt) REVERT: H 383 MET cc_start: 0.3749 (mtt) cc_final: 0.3329 (ptt) REVERT: H 433 GLU cc_start: 0.3871 (tt0) cc_final: 0.2841 (mp0) REVERT: H 459 TRP cc_start: 0.2157 (t60) cc_final: 0.1581 (t60) REVERT: H 462 MET cc_start: 0.0402 (mmp) cc_final: -0.0222 (ttp) REVERT: H 578 ASN cc_start: 0.4177 (p0) cc_final: 0.3817 (m-40) outliers start: 0 outliers final: 2 residues processed: 397 average time/residue: 0.7331 time to fit residues: 354.7409 Evaluate side-chains 197 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain F residue 474 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 540 ASN A 762 ASN A 912 ASN B 491 GLN B 802 GLN C 66 HIS C 243 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 380 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN G 417 HIS G 531 GLN H 117 ASN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN H 572 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.225971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.165335 restraints weight = 64724.113| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 4.75 r_work: 0.3227 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41015 Z= 0.125 Angle : 0.579 9.696 55958 Z= 0.291 Chirality : 0.044 0.256 6396 Planarity : 0.004 0.045 7079 Dihedral : 8.042 90.624 7160 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer: Outliers : 0.96 % Allowed : 7.87 % Favored : 91.18 % 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: 0.11 (0.12), residues: 4815 helix: 1.64 (0.13), residues: 1722 sheet: 0.45 (0.19), residues: 715 loop : -1.28 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 460 TYR 0.019 0.001 TYR G 183 PHE 0.017 0.001 PHE B 904 TRP 0.018 0.001 TRP H 461 HIS 0.009 0.001 HIS H 505 Details of bonding type rmsd covalent geometry : bond 0.00276 (40876) covalent geometry : angle 0.56231 (55589) SS BOND : bond 0.00332 ( 48) SS BOND : angle 1.39246 ( 96) hydrogen bonds : bond 0.05025 ( 1709) hydrogen bonds : angle 4.81448 ( 4830) link_BETA1-4 : bond 0.00448 ( 38) link_BETA1-4 : angle 2.09601 ( 114) link_NAG-ASN : bond 0.00270 ( 53) link_NAG-ASN : angle 1.81436 ( 159) *********************** 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 267 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6937 (p0) cc_final: 0.6560 (p0) REVERT: A 198 TYR cc_start: 0.8424 (m-80) cc_final: 0.7994 (m-80) REVERT: A 235 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7560 (mtm180) REVERT: A 738 MET cc_start: 0.9300 (ttt) cc_final: 0.9008 (ttm) REVERT: B 81 ASN cc_start: 0.7450 (m-40) cc_final: 0.6795 (p0) REVERT: B 569 ASP cc_start: 0.8101 (t0) cc_final: 0.7855 (t0) REVERT: B 853 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7515 (p90) REVERT: B 1140 GLN cc_start: 0.8900 (mm110) cc_final: 0.8620 (mm-40) REVERT: C 186 ASN cc_start: 0.6960 (m-40) cc_final: 0.6006 (p0) REVERT: C 540 ASN cc_start: 0.8037 (p0) cc_final: 0.7832 (t0) REVERT: F 62 MET cc_start: 0.3415 (mmt) cc_final: 0.1723 (mtp) REVERT: F 123 MET cc_start: -0.0321 (ptp) cc_final: -0.0932 (ttm) REVERT: F 462 MET cc_start: 0.3799 (mpp) cc_final: 0.3449 (mmp) REVERT: F 510 TYR cc_start: 0.5775 (m-80) cc_final: 0.5491 (m-10) REVERT: F 531 GLN cc_start: 0.6691 (mp10) cc_final: 0.5953 (pt0) REVERT: F 579 MET cc_start: 0.0342 (mtp) cc_final: -0.1031 (mpp) REVERT: G 82 MET cc_start: 0.0411 (pmm) cc_final: -0.0076 (ttp) REVERT: G 95 LEU cc_start: 0.3436 (tt) cc_final: 0.3122 (pp) REVERT: G 123 MET cc_start: 0.0002 (ptt) cc_final: -0.0753 (ttp) REVERT: G 192 ARG cc_start: 0.4139 (mpp-170) cc_final: 0.3717 (ptp-170) REVERT: G 249 MET cc_start: 0.0975 (mmt) cc_final: -0.0887 (tmm) REVERT: G 297 MET cc_start: -0.0116 (tpp) cc_final: -0.0654 (ttm) REVERT: G 323 MET cc_start: -0.0324 (tpt) cc_final: -0.0846 (tpt) REVERT: G 408 MET cc_start: 0.2820 (pmm) cc_final: 0.1326 (mmm) REVERT: G 557 MET cc_start: 0.5593 (ppp) cc_final: 0.5244 (tpt) REVERT: H 62 MET cc_start: 0.4705 (mtm) cc_final: 0.4471 (mtt) REVERT: H 94 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6777 (ptmm) REVERT: H 156 LEU cc_start: 0.2492 (tp) cc_final: 0.2153 (mm) REVERT: H 270 MET cc_start: -0.0116 (mtt) cc_final: -0.0896 (mmt) REVERT: H 366 MET cc_start: 0.2650 (tpt) cc_final: 0.1377 (tpt) REVERT: H 383 MET cc_start: 0.3498 (mtt) cc_final: 0.3203 (ptt) REVERT: H 433 GLU cc_start: 0.3815 (tt0) cc_final: 0.2842 (mp0) REVERT: H 462 MET cc_start: 0.0542 (mmp) cc_final: -0.0126 (ttm) REVERT: H 476 LYS cc_start: 0.6499 (mmmt) cc_final: 0.6115 (ttmt) outliers start: 41 outliers final: 9 residues processed: 250 average time/residue: 0.7453 time to fit residues: 225.4849 Evaluate side-chains 191 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 152 MET Chi-restraints excluded: chain H residue 295 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 261 optimal weight: 0.3980 chunk 266 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 912 ASN A 963 GLN B 912 ASN C 639 ASN C 749 ASN C 912 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS H 117 ASN H 194 ASN H 239 HIS H 330 ASN H 531 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.225019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.163339 restraints weight = 64146.007| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 4.77 r_work: 0.3164 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41015 Z= 0.151 Angle : 0.580 13.482 55958 Z= 0.289 Chirality : 0.045 0.244 6396 Planarity : 0.004 0.052 7079 Dihedral : 7.526 87.883 7155 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 1.17 % Allowed : 11.35 % Favored : 87.48 % 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: 0.04 (0.12), residues: 4815 helix: 1.54 (0.13), residues: 1723 sheet: 0.47 (0.19), residues: 719 loop : -1.32 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 482 TYR 0.021 0.001 TYR C1065 PHE 0.020 0.001 PHE C 757 TRP 0.035 0.001 TRP B 434 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00363 (40876) covalent geometry : angle 0.56162 (55589) SS BOND : bond 0.00383 ( 48) SS BOND : angle 1.39636 ( 96) hydrogen bonds : bond 0.05347 ( 1709) hydrogen bonds : angle 4.69182 ( 4830) link_BETA1-4 : bond 0.00391 ( 38) link_BETA1-4 : angle 2.12886 ( 114) link_NAG-ASN : bond 0.00270 ( 53) link_NAG-ASN : angle 1.87841 ( 159) *********************** 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 245 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6915 (p0) cc_final: 0.6597 (p0) REVERT: A 198 TYR cc_start: 0.8543 (m-80) cc_final: 0.8245 (m-80) REVERT: A 738 MET cc_start: 0.9329 (ttt) cc_final: 0.9036 (ttm) REVERT: B 81 ASN cc_start: 0.7400 (m-40) cc_final: 0.6651 (p0) REVERT: B 569 ASP cc_start: 0.8057 (t0) cc_final: 0.7764 (t0) REVERT: B 1140 GLN cc_start: 0.8926 (mm110) cc_final: 0.8684 (mm-40) REVERT: C 186 ASN cc_start: 0.6785 (m-40) cc_final: 0.6014 (p0) REVERT: F 62 MET cc_start: 0.3410 (mmt) cc_final: 0.1681 (mtp) REVERT: F 123 MET cc_start: -0.0401 (ptp) cc_final: -0.0944 (ttp) REVERT: F 462 MET cc_start: 0.4239 (mpp) cc_final: 0.3811 (mmt) REVERT: F 474 MET cc_start: -0.0804 (OUTLIER) cc_final: -0.1204 (tpp) REVERT: F 510 TYR cc_start: 0.5740 (m-80) cc_final: 0.5511 (m-10) REVERT: F 531 GLN cc_start: 0.6475 (mp10) cc_final: 0.5866 (pt0) REVERT: F 557 MET cc_start: 0.5547 (ttm) cc_final: 0.5192 (tpt) REVERT: F 579 MET cc_start: 0.0345 (mtp) cc_final: -0.1083 (mpp) REVERT: G 82 MET cc_start: 0.1130 (pmm) cc_final: 0.0899 (ttp) REVERT: G 95 LEU cc_start: 0.3473 (tt) cc_final: 0.3172 (pp) REVERT: G 123 MET cc_start: -0.0012 (ptt) cc_final: -0.0752 (ttp) REVERT: G 192 ARG cc_start: 0.4115 (mpp-170) cc_final: 0.3570 (ptp-170) REVERT: G 249 MET cc_start: 0.1059 (mmt) cc_final: -0.0855 (tmm) REVERT: G 297 MET cc_start: 0.0034 (tpp) cc_final: -0.0619 (ttm) REVERT: G 312 GLU cc_start: 0.4325 (tt0) cc_final: 0.3912 (pt0) REVERT: G 323 MET cc_start: -0.0426 (tpt) cc_final: -0.0686 (tpt) REVERT: G 408 MET cc_start: 0.2856 (pmm) cc_final: 0.1480 (mmm) REVERT: G 480 MET cc_start: 0.3580 (mtt) cc_final: 0.2690 (mmm) REVERT: G 557 MET cc_start: 0.5577 (ppp) cc_final: 0.5252 (tpt) REVERT: H 110 GLU cc_start: 0.4169 (tm-30) cc_final: 0.3869 (pm20) REVERT: H 156 LEU cc_start: 0.2560 (tp) cc_final: 0.2240 (mm) REVERT: H 190 MET cc_start: 0.3404 (OUTLIER) cc_final: 0.3158 (tpt) REVERT: H 270 MET cc_start: -0.0221 (mtt) cc_final: -0.1233 (mmt) REVERT: H 366 MET cc_start: 0.2721 (tpt) cc_final: 0.1461 (tpt) REVERT: H 383 MET cc_start: 0.3621 (mtt) cc_final: 0.3242 (ptt) REVERT: H 433 GLU cc_start: 0.3834 (tt0) cc_final: 0.2870 (mp0) REVERT: H 462 MET cc_start: 0.0513 (mmp) cc_final: -0.0136 (ttm) REVERT: H 476 LYS cc_start: 0.6431 (mmmt) cc_final: 0.6114 (ttmt) outliers start: 50 outliers final: 20 residues processed: 226 average time/residue: 0.6856 time to fit residues: 190.8411 Evaluate side-chains 202 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 933 GLN Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 376 MET Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 152 MET Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 295 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 235 optimal weight: 0.0170 chunk 447 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 349 optimal weight: 0.1980 chunk 466 optimal weight: 5.9990 chunk 439 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 chunk 167 optimal weight: 0.0970 chunk 237 optimal weight: 20.0000 overall best weight: 1.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 912 ASN C 352 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.224503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.162159 restraints weight = 63868.169| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 4.77 r_work: 0.3148 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41015 Z= 0.173 Angle : 0.592 10.020 55958 Z= 0.295 Chirality : 0.045 0.258 6396 Planarity : 0.004 0.075 7079 Dihedral : 7.271 83.884 7155 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 1.87 % Allowed : 12.99 % Favored : 85.14 % 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: 1.50 (0.13), residues: 1723 sheet: 0.44 (0.19), residues: 709 loop : -1.30 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1037 TYR 0.022 0.001 TYR C1065 PHE 0.018 0.001 PHE C 757 TRP 0.026 0.001 TRP A 64 HIS 0.006 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00422 (40876) covalent geometry : angle 0.57216 (55589) SS BOND : bond 0.00416 ( 48) SS BOND : angle 1.73326 ( 96) hydrogen bonds : bond 0.05567 ( 1709) hydrogen bonds : angle 4.66620 ( 4830) link_BETA1-4 : bond 0.00359 ( 38) link_BETA1-4 : angle 2.08688 ( 114) link_NAG-ASN : bond 0.00268 ( 53) link_NAG-ASN : angle 1.95105 ( 159) *********************** 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 273 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 1.621 Fit side-chains REVERT: A 198 TYR cc_start: 0.8720 (m-80) cc_final: 0.8069 (m-80) REVERT: A 932 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 1037 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8480 (mtp180) REVERT: B 81 ASN cc_start: 0.7504 (m-40) cc_final: 0.6765 (p0) REVERT: B 240 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7272 (mp) REVERT: B 569 ASP cc_start: 0.8098 (t0) cc_final: 0.7840 (t0) REVERT: B 1140 GLN cc_start: 0.8951 (mm110) cc_final: 0.8693 (mm-40) REVERT: C 499 ASN cc_start: 0.4119 (OUTLIER) cc_final: 0.0277 (t0) REVERT: F 62 MET cc_start: 0.3140 (mmt) cc_final: 0.1732 (mtp) REVERT: F 123 MET cc_start: -0.0643 (ptp) cc_final: -0.1103 (ttp) REVERT: F 462 MET cc_start: 0.4575 (mpp) cc_final: 0.4169 (mmt) REVERT: F 474 MET cc_start: -0.0933 (OUTLIER) cc_final: -0.1329 (tpp) REVERT: F 510 TYR cc_start: 0.5730 (m-80) cc_final: 0.5503 (m-10) REVERT: F 531 GLN cc_start: 0.6520 (mp10) cc_final: 0.5842 (pt0) REVERT: F 557 MET cc_start: 0.5572 (ttm) cc_final: 0.5144 (tpt) REVERT: F 579 MET cc_start: 0.0160 (mtp) cc_final: -0.1102 (mtm) REVERT: G 82 MET cc_start: 0.1028 (pmm) cc_final: 0.0765 (ttp) REVERT: G 95 LEU cc_start: 0.3837 (tt) cc_final: 0.3487 (pp) REVERT: G 123 MET cc_start: -0.0208 (ptt) cc_final: -0.0824 (ttp) REVERT: G 192 ARG cc_start: 0.4120 (mpp-170) cc_final: 0.3514 (ptp-170) REVERT: G 249 MET cc_start: 0.0912 (mmt) cc_final: -0.1050 (tmm) REVERT: G 297 MET cc_start: 0.0229 (tpp) cc_final: -0.0448 (ttm) REVERT: G 312 GLU cc_start: 0.4167 (tt0) cc_final: 0.3889 (pt0) REVERT: G 323 MET cc_start: -0.0420 (tpt) cc_final: -0.0674 (tpt) REVERT: G 408 MET cc_start: 0.2847 (pmm) cc_final: 0.1442 (mmm) REVERT: G 480 MET cc_start: 0.3313 (mtt) cc_final: 0.2426 (mmm) REVERT: H 82 MET cc_start: 0.3512 (pmm) cc_final: 0.2794 (tmm) REVERT: H 110 GLU cc_start: 0.4040 (tm-30) cc_final: 0.3721 (pm20) REVERT: H 156 LEU cc_start: 0.2562 (tp) cc_final: 0.2170 (mm) REVERT: H 249 MET cc_start: 0.2058 (pmm) cc_final: 0.1114 (ptm) REVERT: H 270 MET cc_start: -0.0141 (mtt) cc_final: -0.0526 (mmt) REVERT: H 366 MET cc_start: 0.2680 (tpt) cc_final: 0.1481 (tpt) REVERT: H 383 MET cc_start: 0.3669 (mtt) cc_final: 0.3259 (ptt) REVERT: H 433 GLU cc_start: 0.3873 (tt0) cc_final: 0.2881 (mp0) REVERT: H 462 MET cc_start: 0.0508 (mmp) cc_final: -0.0163 (ttm) REVERT: H 476 LYS cc_start: 0.6414 (mmmt) cc_final: 0.6084 (ttmt) outliers start: 80 outliers final: 29 residues processed: 254 average time/residue: 0.6503 time to fit residues: 205.1562 Evaluate side-chains 208 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 295 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 310 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 426 optimal weight: 20.0000 chunk 303 optimal weight: 0.0970 chunk 431 optimal weight: 30.0000 chunk 198 optimal weight: 0.9980 chunk 290 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN A 540 ASN A 912 ASN C 186 ASN C 540 ASN C 639 ASN C 912 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.225970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.165098 restraints weight = 64226.456| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 4.84 r_work: 0.3197 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 41015 Z= 0.108 Angle : 0.544 11.952 55958 Z= 0.267 Chirality : 0.043 0.253 6396 Planarity : 0.004 0.090 7079 Dihedral : 6.796 80.000 7155 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 1.69 % Allowed : 14.40 % Favored : 83.92 % 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: 0.20 (0.12), residues: 4815 helix: 1.64 (0.13), residues: 1726 sheet: 0.56 (0.19), residues: 717 loop : -1.19 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 460 TYR 0.018 0.001 TYR G 385 PHE 0.017 0.001 PHE C 757 TRP 0.026 0.001 TRP A 64 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00238 (40876) covalent geometry : angle 0.52551 (55589) SS BOND : bond 0.00276 ( 48) SS BOND : angle 1.41532 ( 96) hydrogen bonds : bond 0.04399 ( 1709) hydrogen bonds : angle 4.47096 ( 4830) link_BETA1-4 : bond 0.00391 ( 38) link_BETA1-4 : angle 2.06302 ( 114) link_NAG-ASN : bond 0.00244 ( 53) link_NAG-ASN : angle 1.78519 ( 159) *********************** 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 259 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 187 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6785 (p0) cc_final: 0.6511 (p0) REVERT: A 198 TYR cc_start: 0.8576 (m-80) cc_final: 0.8094 (m-80) REVERT: A 955 GLN cc_start: 0.8929 (tt0) cc_final: 0.8655 (tt0) REVERT: A 1008 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: B 81 ASN cc_start: 0.7436 (m-40) cc_final: 0.6765 (p0) REVERT: B 240 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7076 (mp) REVERT: B 569 ASP cc_start: 0.8047 (t0) cc_final: 0.7785 (t0) REVERT: B 856 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 1140 GLN cc_start: 0.8984 (mm110) cc_final: 0.8731 (mm-40) REVERT: C 186 ASN cc_start: 0.6310 (OUTLIER) cc_final: 0.5540 (p0) REVERT: C 499 ASN cc_start: 0.4095 (OUTLIER) cc_final: 0.0242 (t0) REVERT: C 757 PHE cc_start: 0.7653 (p90) cc_final: 0.7042 (t80) REVERT: F 62 MET cc_start: 0.3460 (mmt) cc_final: 0.2084 (mtp) REVERT: F 123 MET cc_start: -0.0649 (ptp) cc_final: -0.1114 (ttp) REVERT: F 462 MET cc_start: 0.4581 (mpp) cc_final: 0.4271 (mmt) REVERT: F 474 MET cc_start: -0.0966 (OUTLIER) cc_final: -0.1254 (tpp) REVERT: F 531 GLN cc_start: 0.6550 (mp10) cc_final: 0.5963 (pt0) REVERT: F 557 MET cc_start: 0.5611 (ttm) cc_final: 0.5227 (tpt) REVERT: F 579 MET cc_start: 0.0696 (mtp) cc_final: -0.0628 (mtm) REVERT: G 82 MET cc_start: 0.0844 (pmm) cc_final: 0.0628 (ttp) REVERT: G 95 LEU cc_start: 0.3460 (tt) cc_final: 0.3171 (pp) REVERT: G 123 MET cc_start: -0.0227 (ptt) cc_final: -0.0810 (ttp) REVERT: G 192 ARG cc_start: 0.4350 (mpp-170) cc_final: 0.3737 (ptp-170) REVERT: G 249 MET cc_start: 0.0468 (mmt) cc_final: -0.1249 (tmm) REVERT: G 297 MET cc_start: 0.0184 (tpp) cc_final: -0.0456 (ttm) REVERT: G 312 GLU cc_start: 0.4247 (tt0) cc_final: 0.3900 (tp30) REVERT: G 323 MET cc_start: -0.0333 (tpt) cc_final: -0.0890 (tpt) REVERT: G 408 MET cc_start: 0.2541 (pmm) cc_final: 0.1299 (mmm) REVERT: G 480 MET cc_start: 0.3138 (mtt) cc_final: 0.2347 (mmm) REVERT: G 557 MET cc_start: 0.5851 (pp-130) cc_final: 0.5325 (tpt) REVERT: H 82 MET cc_start: 0.3608 (pmm) cc_final: 0.2910 (tmm) REVERT: H 110 GLU cc_start: 0.4192 (tm-30) cc_final: 0.3854 (pm20) REVERT: H 156 LEU cc_start: 0.2637 (tp) cc_final: 0.2245 (mm) REVERT: H 190 MET cc_start: 0.3245 (OUTLIER) cc_final: 0.2985 (tpt) REVERT: H 249 MET cc_start: 0.2148 (pmm) cc_final: 0.1245 (ptm) REVERT: H 270 MET cc_start: -0.0474 (mtt) cc_final: -0.0916 (mmt) REVERT: H 366 MET cc_start: 0.2653 (tpt) cc_final: 0.1381 (tpt) REVERT: H 383 MET cc_start: 0.3691 (mtt) cc_final: 0.3261 (ptt) REVERT: H 433 GLU cc_start: 0.3754 (tt0) cc_final: 0.2874 (mp0) REVERT: H 462 MET cc_start: 0.0778 (mmp) cc_final: 0.0151 (ttm) REVERT: H 476 LYS cc_start: 0.6403 (mmmt) cc_final: 0.6083 (ttmt) outliers start: 72 outliers final: 19 residues processed: 244 average time/residue: 0.6452 time to fit residues: 196.6678 Evaluate side-chains 199 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 190 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 53 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 330 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 439 optimal weight: 40.0000 chunk 101 optimal weight: 0.5980 chunk 465 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 323 optimal weight: 30.0000 chunk 253 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 912 ASN B 499 ASN B 912 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.225296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.164023 restraints weight = 64115.139| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 4.73 r_work: 0.3169 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 41015 Z= 0.132 Angle : 0.562 14.284 55958 Z= 0.276 Chirality : 0.044 0.256 6396 Planarity : 0.004 0.076 7079 Dihedral : 6.672 77.534 7155 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 1.85 % Allowed : 15.15 % Favored : 83.01 % 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: 1.69 (0.13), residues: 1717 sheet: 0.60 (0.19), residues: 710 loop : -1.21 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 460 TYR 0.020 0.001 TYR C1065 PHE 0.016 0.001 PHE A 641 TRP 0.022 0.001 TRP H 163 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (40876) covalent geometry : angle 0.54390 (55589) SS BOND : bond 0.00358 ( 48) SS BOND : angle 1.43616 ( 96) hydrogen bonds : bond 0.04839 ( 1709) hydrogen bonds : angle 4.47856 ( 4830) link_BETA1-4 : bond 0.00365 ( 38) link_BETA1-4 : angle 2.04520 ( 114) link_NAG-ASN : bond 0.00245 ( 53) link_NAG-ASN : angle 1.84797 ( 159) *********************** 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 263 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6505 (p0) REVERT: A 198 TYR cc_start: 0.8601 (m-80) cc_final: 0.8131 (m-80) REVERT: A 597 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9127 (p) REVERT: A 738 MET cc_start: 0.9314 (ttt) cc_final: 0.9021 (ttm) REVERT: A 955 GLN cc_start: 0.8918 (tt0) cc_final: 0.8652 (tt0) REVERT: A 1008 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: A 1037 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8494 (mtp180) REVERT: B 81 ASN cc_start: 0.7463 (m-40) cc_final: 0.6868 (p0) REVERT: B 240 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7111 (mp) REVERT: B 569 ASP cc_start: 0.8024 (t0) cc_final: 0.7740 (t0) REVERT: B 1140 GLN cc_start: 0.9002 (mm110) cc_final: 0.8769 (mm-40) REVERT: C 186 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.5679 (p0) REVERT: C 499 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.0435 (t0) REVERT: C 609 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8810 (tp) REVERT: C 778 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: C 979 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8894 (mp) REVERT: F 62 MET cc_start: 0.3294 (mmp) cc_final: 0.1964 (mtp) REVERT: F 123 MET cc_start: -0.0650 (ptp) cc_final: -0.1108 (ttt) REVERT: F 462 MET cc_start: 0.4850 (mpp) cc_final: 0.4524 (mmt) REVERT: F 474 MET cc_start: -0.1001 (OUTLIER) cc_final: -0.1396 (tpp) REVERT: F 531 GLN cc_start: 0.6546 (mp10) cc_final: 0.5923 (pt0) REVERT: F 557 MET cc_start: 0.5570 (ttm) cc_final: 0.5155 (tpt) REVERT: F 579 MET cc_start: 0.0685 (mtp) cc_final: -0.0668 (mtm) REVERT: G 95 LEU cc_start: 0.3463 (tt) cc_final: 0.3174 (pp) REVERT: G 123 MET cc_start: -0.0260 (ptt) cc_final: -0.0862 (ttp) REVERT: G 192 ARG cc_start: 0.4392 (mpp-170) cc_final: 0.3774 (ptp-170) REVERT: G 249 MET cc_start: 0.0454 (mmt) cc_final: -0.1287 (tmm) REVERT: G 297 MET cc_start: 0.0239 (tpp) cc_final: -0.0407 (ttm) REVERT: G 309 LYS cc_start: 0.6534 (mttm) cc_final: 0.6269 (ttpt) REVERT: G 312 GLU cc_start: 0.4411 (tt0) cc_final: 0.4102 (tp30) REVERT: G 323 MET cc_start: -0.0346 (tpt) cc_final: -0.0900 (tpt) REVERT: G 408 MET cc_start: 0.2542 (pmm) cc_final: 0.1312 (mmm) REVERT: G 455 MET cc_start: 0.3377 (pp-130) cc_final: 0.2549 (pp-130) REVERT: G 477 TRP cc_start: 0.1277 (OUTLIER) cc_final: 0.0893 (t60) REVERT: G 480 MET cc_start: 0.3136 (mtt) cc_final: 0.2270 (mmp) REVERT: G 557 MET cc_start: 0.5658 (pp-130) cc_final: 0.5136 (tpt) REVERT: H 82 MET cc_start: 0.3640 (pmm) cc_final: 0.2739 (tmm) REVERT: H 110 GLU cc_start: 0.4185 (tm-30) cc_final: 0.3868 (pm20) REVERT: H 156 LEU cc_start: 0.2632 (tp) cc_final: 0.2246 (mm) REVERT: H 190 MET cc_start: 0.3224 (OUTLIER) cc_final: 0.2948 (tpt) REVERT: H 249 MET cc_start: 0.2331 (pmm) cc_final: 0.1382 (ptm) REVERT: H 270 MET cc_start: -0.0286 (mtt) cc_final: -0.0607 (mmt) REVERT: H 366 MET cc_start: 0.2654 (tpt) cc_final: 0.1399 (tpt) REVERT: H 383 MET cc_start: 0.3660 (mtt) cc_final: 0.3307 (ptt) REVERT: H 433 GLU cc_start: 0.3758 (tt0) cc_final: 0.2871 (mp0) REVERT: H 462 MET cc_start: 0.0948 (mmp) cc_final: 0.0265 (ttm) REVERT: H 476 LYS cc_start: 0.6293 (mmmt) cc_final: 0.5974 (ttmt) outliers start: 79 outliers final: 32 residues processed: 244 average time/residue: 0.6149 time to fit residues: 186.0334 Evaluate side-chains 218 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 643 THR 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 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 477 TRP Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 354 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 482 optimal weight: 0.0970 chunk 212 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 387 optimal weight: 50.0000 chunk 156 optimal weight: 2.9990 chunk 365 optimal weight: 30.0000 chunk 245 optimal weight: 0.0170 overall best weight: 2.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN C 186 ASN C 912 ASN F 137 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 90 ASN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.224708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.163545 restraints weight = 63759.891| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 4.78 r_work: 0.3124 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 41015 Z= 0.210 Angle : 0.630 10.898 55958 Z= 0.312 Chirality : 0.046 0.299 6396 Planarity : 0.004 0.071 7079 Dihedral : 6.808 75.333 7155 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.17 % Favored : 94.81 % Rotamer: Outliers : 2.29 % Allowed : 15.05 % Favored : 82.65 % 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: 0.05 (0.12), residues: 4815 helix: 1.58 (0.13), residues: 1711 sheet: 0.51 (0.19), residues: 707 loop : -1.33 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1037 TYR 0.024 0.001 TYR C1065 PHE 0.021 0.002 PHE C 757 TRP 0.019 0.001 TRP A 64 HIS 0.007 0.001 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00523 (40876) covalent geometry : angle 0.61074 (55589) SS BOND : bond 0.00462 ( 48) SS BOND : angle 1.78639 ( 96) hydrogen bonds : bond 0.05988 ( 1709) hydrogen bonds : angle 4.62091 ( 4830) link_BETA1-4 : bond 0.00356 ( 38) link_BETA1-4 : angle 2.12285 ( 114) link_NAG-ASN : bond 0.00318 ( 53) link_NAG-ASN : angle 2.02649 ( 159) *********************** 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 283 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 185 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6714 (p0) REVERT: A 198 TYR cc_start: 0.8628 (m-80) cc_final: 0.8147 (m-80) REVERT: A 235 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7117 (mpp80) REVERT: A 597 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9171 (p) REVERT: A 738 MET cc_start: 0.9351 (ttt) cc_final: 0.9071 (ttp) REVERT: A 1037 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8485 (mtp180) REVERT: B 81 ASN cc_start: 0.7525 (m-40) cc_final: 0.6565 (p0) REVERT: B 237 GLN cc_start: 0.8233 (tt0) cc_final: 0.7877 (tp40) REVERT: B 240 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7110 (mp) REVERT: B 569 ASP cc_start: 0.8046 (t0) cc_final: 0.7794 (t0) REVERT: B 856 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8871 (pp) REVERT: B 1140 GLN cc_start: 0.9006 (mm110) cc_final: 0.8759 (mm-40) REVERT: C 499 ASN cc_start: 0.4449 (OUTLIER) cc_final: 0.0620 (t0) REVERT: C 558 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (mp) REVERT: C 609 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 668 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8605 (pt) REVERT: F 32 PHE cc_start: 0.7487 (t80) cc_final: 0.7181 (t80) REVERT: F 62 MET cc_start: 0.3189 (mmp) cc_final: 0.1866 (mtp) REVERT: F 123 MET cc_start: -0.0652 (ptp) cc_final: -0.1125 (ttp) REVERT: F 462 MET cc_start: 0.4869 (mpp) cc_final: 0.4555 (mmt) REVERT: F 474 MET cc_start: -0.0974 (OUTLIER) cc_final: -0.1324 (tpp) REVERT: F 531 GLN cc_start: 0.6527 (mp10) cc_final: 0.5875 (pt0) REVERT: F 579 MET cc_start: 0.0493 (mtp) cc_final: -0.0915 (mtm) REVERT: G 95 LEU cc_start: 0.3833 (tt) cc_final: 0.3497 (pp) REVERT: G 123 MET cc_start: -0.0310 (ptt) cc_final: -0.0934 (ttp) REVERT: G 192 ARG cc_start: 0.4424 (mpp-170) cc_final: 0.3786 (ptp-170) REVERT: G 231 GLU cc_start: 0.4333 (mm-30) cc_final: 0.3622 (mp0) REVERT: G 249 MET cc_start: 0.0724 (mmt) cc_final: -0.1308 (tmm) REVERT: G 297 MET cc_start: 0.0252 (tpp) cc_final: -0.0387 (ttm) REVERT: G 312 GLU cc_start: 0.4411 (tt0) cc_final: 0.4068 (tp30) REVERT: G 323 MET cc_start: -0.0238 (tpt) cc_final: -0.0743 (tpt) REVERT: G 477 TRP cc_start: 0.1258 (OUTLIER) cc_final: 0.0902 (t60) REVERT: G 480 MET cc_start: 0.2762 (mtt) cc_final: 0.1944 (mmp) REVERT: G 557 MET cc_start: 0.5450 (pp-130) cc_final: 0.4932 (tpt) REVERT: H 82 MET cc_start: 0.3369 (pmm) cc_final: 0.2624 (tmm) REVERT: H 110 GLU cc_start: 0.4081 (tm-30) cc_final: 0.3728 (pt0) REVERT: H 156 LEU cc_start: 0.2640 (tp) cc_final: 0.2244 (mm) REVERT: H 190 MET cc_start: 0.3154 (OUTLIER) cc_final: 0.2948 (tpt) REVERT: H 249 MET cc_start: 0.2337 (pmm) cc_final: 0.1385 (ptm) REVERT: H 270 MET cc_start: -0.0516 (mtt) cc_final: -0.0783 (mmt) REVERT: H 323 MET cc_start: 0.0429 (tpp) cc_final: 0.0183 (ppp) REVERT: H 366 MET cc_start: 0.2675 (tpt) cc_final: 0.1575 (tpt) REVERT: H 383 MET cc_start: 0.3459 (mtt) cc_final: 0.2735 (ptt) REVERT: H 433 GLU cc_start: 0.3734 (tt0) cc_final: 0.2821 (mp0) REVERT: H 462 MET cc_start: 0.0983 (mmp) cc_final: 0.0208 (ttm) REVERT: H 471 ASP cc_start: 0.6052 (t0) cc_final: 0.5815 (t0) REVERT: H 476 LYS cc_start: 0.6440 (mmmt) cc_final: 0.6128 (ttmt) outliers start: 98 outliers final: 45 residues processed: 262 average time/residue: 0.6237 time to fit residues: 201.9842 Evaluate side-chains 229 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 477 TRP Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 69 optimal weight: 0.9990 chunk 455 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 274 optimal weight: 0.6980 chunk 449 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 418 optimal weight: 6.9990 chunk 295 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 307 optimal weight: 20.0000 chunk 427 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 540 ASN B 205 HIS ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 442 GLN H 90 ASN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.225621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.164782 restraints weight = 63919.818| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 4.89 r_work: 0.3198 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 41015 Z= 0.110 Angle : 0.554 10.868 55958 Z= 0.272 Chirality : 0.043 0.270 6396 Planarity : 0.004 0.054 7079 Dihedral : 6.349 71.577 7155 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.36 % Favored : 95.62 % Rotamer: Outliers : 1.64 % Allowed : 15.78 % Favored : 82.58 % 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: 0.21 (0.12), residues: 4815 helix: 1.71 (0.13), residues: 1722 sheet: 0.59 (0.19), residues: 678 loop : -1.22 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 188 TYR 0.018 0.001 TYR G 385 PHE 0.016 0.001 PHE A 641 TRP 0.028 0.001 TRP H 163 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00246 (40876) covalent geometry : angle 0.53481 (55589) SS BOND : bond 0.00333 ( 48) SS BOND : angle 1.67103 ( 96) hydrogen bonds : bond 0.04446 ( 1709) hydrogen bonds : angle 4.44362 ( 4830) link_BETA1-4 : bond 0.00407 ( 38) link_BETA1-4 : angle 2.07123 ( 114) link_NAG-ASN : bond 0.00247 ( 53) link_NAG-ASN : angle 1.81486 ( 159) *********************** 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 257 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6910 (p0) cc_final: 0.6648 (p0) REVERT: A 198 TYR cc_start: 0.8600 (m-80) cc_final: 0.8157 (m-80) REVERT: A 597 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9151 (p) REVERT: A 955 GLN cc_start: 0.8910 (tt0) cc_final: 0.8626 (tt0) REVERT: A 1037 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8287 (mtp180) REVERT: B 64 TRP cc_start: 0.7937 (t60) cc_final: 0.7625 (t60) REVERT: B 81 ASN cc_start: 0.7637 (m-40) cc_final: 0.7005 (p0) REVERT: B 240 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7035 (mp) REVERT: B 569 ASP cc_start: 0.7992 (t0) cc_final: 0.7740 (t0) REVERT: B 856 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 1140 GLN cc_start: 0.9011 (mm110) cc_final: 0.8765 (mm-40) REVERT: C 499 ASN cc_start: 0.4420 (OUTLIER) cc_final: 0.0520 (t0) REVERT: C 668 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8516 (pt) REVERT: F 62 MET cc_start: 0.3336 (mmp) cc_final: 0.1976 (mtp) REVERT: F 123 MET cc_start: -0.0555 (ptp) cc_final: -0.1025 (ttt) REVERT: F 462 MET cc_start: 0.4591 (OUTLIER) cc_final: 0.4295 (mmt) REVERT: F 474 MET cc_start: -0.1017 (OUTLIER) cc_final: -0.1239 (tpp) REVERT: F 531 GLN cc_start: 0.6555 (mp10) cc_final: 0.5903 (pt0) REVERT: F 557 MET cc_start: 0.5568 (ttm) cc_final: 0.5255 (tpt) REVERT: F 579 MET cc_start: 0.0447 (mtp) cc_final: -0.0943 (mtm) REVERT: G 82 MET cc_start: 0.2367 (ttp) cc_final: 0.2075 (ptm) REVERT: G 95 LEU cc_start: 0.3463 (tt) cc_final: 0.3176 (pp) REVERT: G 123 MET cc_start: -0.0278 (ptt) cc_final: -0.0893 (ttp) REVERT: G 192 ARG cc_start: 0.4441 (mpp-170) cc_final: 0.3782 (ptp-170) REVERT: G 249 MET cc_start: 0.0737 (mmt) cc_final: -0.1343 (tmm) REVERT: G 312 GLU cc_start: 0.4432 (tt0) cc_final: 0.4092 (tp30) REVERT: G 323 MET cc_start: -0.0291 (tpt) cc_final: -0.0790 (tpt) REVERT: G 408 MET cc_start: 0.3057 (pmm) cc_final: 0.1633 (mmm) REVERT: G 477 TRP cc_start: 0.1222 (OUTLIER) cc_final: 0.0840 (t60) REVERT: G 480 MET cc_start: 0.2976 (mtt) cc_final: 0.2202 (mmp) REVERT: G 557 MET cc_start: 0.5413 (pp-130) cc_final: 0.4966 (tpt) REVERT: H 82 MET cc_start: 0.3565 (pmm) cc_final: 0.2642 (tmm) REVERT: H 110 GLU cc_start: 0.4140 (tm-30) cc_final: 0.3855 (pt0) REVERT: H 156 LEU cc_start: 0.2642 (tp) cc_final: 0.2254 (mm) REVERT: H 249 MET cc_start: 0.2663 (pmm) cc_final: 0.1729 (ptm) REVERT: H 270 MET cc_start: -0.0553 (mtt) cc_final: -0.0805 (mmt) REVERT: H 323 MET cc_start: 0.0478 (tpp) cc_final: 0.0233 (ppp) REVERT: H 366 MET cc_start: 0.2656 (tpt) cc_final: 0.1489 (tpt) REVERT: H 383 MET cc_start: 0.3500 (mtt) cc_final: 0.2748 (ptt) REVERT: H 433 GLU cc_start: 0.3712 (tt0) cc_final: 0.2838 (mp0) REVERT: H 462 MET cc_start: 0.0956 (mmp) cc_final: 0.0292 (ttm) REVERT: H 471 ASP cc_start: 0.6017 (t0) cc_final: 0.5606 (t0) REVERT: H 476 LYS cc_start: 0.6304 (mmmt) cc_final: 0.5989 (ttmt) outliers start: 70 outliers final: 36 residues processed: 239 average time/residue: 0.6195 time to fit residues: 184.9785 Evaluate side-chains 215 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 477 TRP Chi-restraints excluded: chain H residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 135 optimal weight: 5.9990 chunk 469 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 332 optimal weight: 50.0000 chunk 85 optimal weight: 7.9990 chunk 478 optimal weight: 1.9990 chunk 466 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN B 437 ASN C 899 GLN C1009 GLN F 239 HIS ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 GLN H 90 ASN H 239 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.221800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.158701 restraints weight = 63324.918| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 4.84 r_work: 0.3081 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 41015 Z= 0.345 Angle : 0.749 10.583 55958 Z= 0.374 Chirality : 0.052 0.375 6396 Planarity : 0.005 0.070 7079 Dihedral : 6.977 71.384 7155 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 1.97 % Allowed : 15.73 % Favored : 82.30 % 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: -0.23 (0.12), residues: 4815 helix: 1.34 (0.13), residues: 1707 sheet: 0.35 (0.19), residues: 676 loop : -1.46 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1037 TYR 0.031 0.002 TYR C1065 PHE 0.029 0.003 PHE A 166 TRP 0.027 0.002 TRP G 610 HIS 0.011 0.002 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00873 (40876) covalent geometry : angle 0.72668 (55589) SS BOND : bond 0.00707 ( 48) SS BOND : angle 2.58427 ( 96) hydrogen bonds : bond 0.07359 ( 1709) hydrogen bonds : angle 4.81617 ( 4830) link_BETA1-4 : bond 0.00370 ( 38) link_BETA1-4 : angle 2.29090 ( 114) link_NAG-ASN : bond 0.00482 ( 53) link_NAG-ASN : angle 2.26471 ( 159) *********************** 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 259 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 175 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7104 (OUTLIER) cc_final: 0.6792 (p0) REVERT: A 198 TYR cc_start: 0.8672 (m-80) cc_final: 0.8187 (m-80) REVERT: A 235 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7081 (mpp80) REVERT: A 894 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8694 (tp) REVERT: A 1037 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8331 (ptm160) REVERT: B 81 ASN cc_start: 0.7694 (m-40) cc_final: 0.6578 (p0) REVERT: B 237 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: B 240 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7126 (mp) REVERT: B 569 ASP cc_start: 0.8175 (t0) cc_final: 0.7962 (t0) REVERT: B 793 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8338 (mtpp) REVERT: B 856 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8900 (pp) REVERT: B 1140 GLN cc_start: 0.9024 (mm110) cc_final: 0.8766 (mm-40) REVERT: C 668 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8765 (pt) REVERT: C 1037 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: C 1142 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: F 62 MET cc_start: 0.3198 (mmp) cc_final: 0.1896 (mtp) REVERT: F 123 MET cc_start: -0.0534 (ptp) cc_final: -0.1051 (ttp) REVERT: F 462 MET cc_start: 0.4359 (OUTLIER) cc_final: 0.4050 (mmt) REVERT: F 474 MET cc_start: -0.1039 (OUTLIER) cc_final: -0.1303 (tpp) REVERT: F 531 GLN cc_start: 0.6601 (mp10) cc_final: 0.5925 (pt0) REVERT: F 557 MET cc_start: 0.5521 (ttm) cc_final: 0.5197 (tpt) REVERT: F 579 MET cc_start: 0.0491 (mtp) cc_final: -0.1053 (mtm) REVERT: G 82 MET cc_start: 0.2323 (ttp) cc_final: 0.2083 (ptm) REVERT: G 95 LEU cc_start: 0.3669 (tt) cc_final: 0.3323 (pp) REVERT: G 123 MET cc_start: -0.0101 (ptt) cc_final: -0.0672 (ttp) REVERT: G 192 ARG cc_start: 0.4483 (mpp-170) cc_final: 0.3772 (ptp-170) REVERT: G 297 MET cc_start: 0.0024 (tpt) cc_final: -0.0827 (ttm) REVERT: G 323 MET cc_start: -0.0319 (tpt) cc_final: -0.0699 (tpt) REVERT: G 408 MET cc_start: 0.2842 (pmm) cc_final: 0.1551 (mmm) REVERT: G 455 MET cc_start: 0.3296 (pp-130) cc_final: 0.2942 (pp-130) REVERT: G 477 TRP cc_start: 0.1478 (OUTLIER) cc_final: 0.1194 (t60) REVERT: G 480 MET cc_start: 0.2834 (mtt) cc_final: 0.2046 (mmp) REVERT: G 557 MET cc_start: 0.5426 (pp-130) cc_final: 0.4944 (tpt) REVERT: H 82 MET cc_start: 0.3379 (pmm) cc_final: 0.2651 (tmm) REVERT: H 110 GLU cc_start: 0.4038 (tm-30) cc_final: 0.3792 (pt0) REVERT: H 156 LEU cc_start: 0.2631 (tp) cc_final: 0.2238 (mm) REVERT: H 249 MET cc_start: 0.2350 (pmm) cc_final: 0.1466 (ptm) REVERT: H 270 MET cc_start: -0.0749 (mtt) cc_final: -0.1022 (mmt) REVERT: H 383 MET cc_start: 0.3480 (mtt) cc_final: 0.3095 (ptt) REVERT: H 433 GLU cc_start: 0.3687 (tt0) cc_final: 0.2718 (mp0) REVERT: H 462 MET cc_start: 0.0672 (mmp) cc_final: 0.0052 (ttm) REVERT: H 471 ASP cc_start: 0.5929 (t0) cc_final: 0.5653 (t0) REVERT: H 476 LYS cc_start: 0.6465 (mmmt) cc_final: 0.6149 (ttmt) outliers start: 84 outliers final: 45 residues processed: 239 average time/residue: 0.6686 time to fit residues: 197.5166 Evaluate side-chains 226 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1037 ARG Chi-restraints excluded: chain C residue 1142 GLU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 477 TRP Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 474 MET Chi-restraints excluded: chain H residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 151 optimal weight: 0.3980 chunk 445 optimal weight: 6.9990 chunk 428 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 397 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN A 912 ASN C 899 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS H 493 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.225810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.165234 restraints weight = 63849.859| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 4.84 r_work: 0.3159 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 41015 Z= 0.116 Angle : 0.571 10.324 55958 Z= 0.281 Chirality : 0.043 0.273 6396 Planarity : 0.004 0.057 7079 Dihedral : 6.357 67.449 7155 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 1.50 % Allowed : 16.36 % Favored : 82.14 % 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: 0.05 (0.12), residues: 4815 helix: 1.59 (0.13), residues: 1717 sheet: 0.50 (0.19), residues: 682 loop : -1.31 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 460 TYR 0.022 0.001 TYR F 158 PHE 0.027 0.001 PHE A 641 TRP 0.026 0.001 TRP G 610 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00259 (40876) covalent geometry : angle 0.55108 (55589) SS BOND : bond 0.00361 ( 48) SS BOND : angle 1.63153 ( 96) hydrogen bonds : bond 0.04801 ( 1709) hydrogen bonds : angle 4.53855 ( 4830) link_BETA1-4 : bond 0.00398 ( 38) link_BETA1-4 : angle 2.12672 ( 114) link_NAG-ASN : bond 0.00238 ( 53) link_NAG-ASN : angle 1.90454 ( 159) ********************** 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: 64 poor density : 176 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7025 (p0) cc_final: 0.6729 (p0) REVERT: A 198 TYR cc_start: 0.8624 (m-80) cc_final: 0.8171 (m-80) REVERT: A 738 MET cc_start: 0.9317 (ttt) cc_final: 0.9034 (ttm) REVERT: A 894 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 955 GLN cc_start: 0.8927 (tt0) cc_final: 0.8645 (tt0) REVERT: A 1037 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8254 (mtp180) REVERT: B 81 ASN cc_start: 0.7695 (m-40) cc_final: 0.6878 (p0) REVERT: B 237 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7792 (tp40) REVERT: B 240 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7026 (mp) REVERT: B 569 ASP cc_start: 0.8051 (t0) cc_final: 0.7830 (t0) REVERT: B 1140 GLN cc_start: 0.9030 (mm110) cc_final: 0.8779 (mm-40) REVERT: C 499 ASN cc_start: 0.4470 (OUTLIER) cc_final: 0.0682 (t0) REVERT: C 668 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8560 (pt) REVERT: C 1037 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8145 (mtp180) REVERT: F 62 MET cc_start: 0.3186 (mmp) cc_final: 0.1898 (mtp) REVERT: F 123 MET cc_start: -0.0626 (ptp) cc_final: -0.1070 (ttt) REVERT: F 462 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.4014 (mmt) REVERT: F 474 MET cc_start: -0.1167 (OUTLIER) cc_final: -0.1400 (tpp) REVERT: F 531 GLN cc_start: 0.6644 (mp10) cc_final: 0.5952 (pt0) REVERT: F 557 MET cc_start: 0.5562 (ttm) cc_final: 0.5241 (tpt) REVERT: F 579 MET cc_start: 0.0400 (mtp) cc_final: -0.1203 (mtm) REVERT: G 95 LEU cc_start: 0.3577 (tt) cc_final: 0.3238 (pp) REVERT: G 123 MET cc_start: -0.0197 (ptt) cc_final: -0.0809 (ttp) REVERT: G 192 ARG cc_start: 0.4529 (mpp-170) cc_final: 0.3781 (ptp-170) REVERT: G 297 MET cc_start: 0.0092 (tpt) cc_final: -0.0777 (ttm) REVERT: G 323 MET cc_start: -0.0346 (tpt) cc_final: -0.0739 (tpt) REVERT: G 408 MET cc_start: 0.2846 (pmm) cc_final: 0.0781 (mmm) REVERT: G 455 MET cc_start: 0.3306 (pp-130) cc_final: 0.2991 (pp-130) REVERT: G 477 TRP cc_start: 0.1329 (OUTLIER) cc_final: 0.1100 (t60) REVERT: G 480 MET cc_start: 0.3020 (mtt) cc_final: 0.2262 (mmp) REVERT: G 557 MET cc_start: 0.5473 (pp-130) cc_final: 0.5019 (tpt) REVERT: H 82 MET cc_start: 0.3572 (pmm) cc_final: 0.2668 (tmm) REVERT: H 156 LEU cc_start: 0.2647 (tp) cc_final: 0.2248 (mm) REVERT: H 249 MET cc_start: 0.2662 (pmm) cc_final: 0.1747 (ptm) REVERT: H 323 MET cc_start: 0.0811 (tpp) cc_final: 0.0319 (ppp) REVERT: H 383 MET cc_start: 0.3471 (mtt) cc_final: 0.2720 (ptt) REVERT: H 433 GLU cc_start: 0.3698 (tt0) cc_final: 0.2810 (mp0) REVERT: H 462 MET cc_start: 0.0974 (mmp) cc_final: 0.0314 (ttp) REVERT: H 471 ASP cc_start: 0.5894 (t0) cc_final: 0.5584 (t0) REVERT: H 476 LYS cc_start: 0.6322 (mmmt) cc_final: 0.5992 (ttmt) outliers start: 64 outliers final: 36 residues processed: 226 average time/residue: 0.6575 time to fit residues: 184.1342 Evaluate side-chains 215 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1037 ARG Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 477 TRP Chi-restraints excluded: chain H residue 474 MET Chi-restraints excluded: chain H residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 292 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 374 optimal weight: 0.0670 chunk 391 optimal weight: 30.0000 chunk 309 optimal weight: 40.0000 chunk 464 optimal weight: 20.0000 chunk 400 optimal weight: 50.0000 chunk 211 optimal weight: 0.2980 chunk 414 optimal weight: 40.0000 chunk 420 optimal weight: 30.0000 overall best weight: 3.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN A 912 ASN C 899 GLN F 194 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN H 239 HIS H 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.221989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.157967 restraints weight = 63495.354| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 4.77 r_work: 0.3079 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 41015 Z= 0.314 Angle : 0.725 10.310 55958 Z= 0.361 Chirality : 0.051 0.380 6396 Planarity : 0.005 0.068 7079 Dihedral : 6.834 66.727 7155 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.86 % Favored : 94.12 % Rotamer: Outliers : 1.64 % Allowed : 16.15 % Favored : 82.21 % 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: -0.31 (0.12), residues: 4815 helix: 1.30 (0.12), residues: 1727 sheet: 0.20 (0.20), residues: 627 loop : -1.48 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1037 TYR 0.030 0.002 TYR C1065 PHE 0.033 0.002 PHE A 641 TRP 0.037 0.002 TRP H 163 HIS 0.010 0.002 HIS B1056 Details of bonding type rmsd covalent geometry : bond 0.00788 (40876) covalent geometry : angle 0.70271 (55589) SS BOND : bond 0.00624 ( 48) SS BOND : angle 2.40170 ( 96) hydrogen bonds : bond 0.07092 ( 1709) hydrogen bonds : angle 4.79352 ( 4830) link_BETA1-4 : bond 0.00373 ( 38) link_BETA1-4 : angle 2.30278 ( 114) link_NAG-ASN : bond 0.00475 ( 53) link_NAG-ASN : angle 2.28187 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18912.62 seconds wall clock time: 321 minutes 23.58 seconds (19283.58 seconds total)