Starting phenix.real_space_refine on Sun Jun 15 11:05:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3d_46532/06_2025/9d3d_46532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3d_46532/06_2025/9d3d_46532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3d_46532/06_2025/9d3d_46532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3d_46532/06_2025/9d3d_46532.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3d_46532/06_2025/9d3d_46532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3d_46532/06_2025/9d3d_46532.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.026 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 119 5.16 5 C 10719 2.51 5 N 2819 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17243 Number of models: 1 Model: "" Number of chains: 50 Chain: "C" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3543 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "A" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3528 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3528 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "c" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "a" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1007 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "b" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {'NAG': 7, 'PO4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "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 Time building chain proxies: 11.28, per 1000 atoms: 0.65 Number of scatterers: 17243 At special positions: 0 Unit cell: (128.65, 124.5, 167.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 1 15.00 O 3585 8.00 N 2819 7.00 C 10719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS a 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS b 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS a 598 " - pdb=" SG CYS a 604 " distance=2.03 Simple disulfide: pdb=" SG CYS b 598 " - pdb=" SG CYS b 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN R 4 " - " MAN R 5 " " MAN p 4 " - " MAN p 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA h 3 " - " MAN h 4 " " BMA l 3 " - " MAN l 4 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 6 " " BMA h 3 " - " MAN h 5 " " BMA p 3 " - " MAN p 6 " " BMA r 3 " - " MAN r 6 " BETA1-3 " NAG m 2 " - " BMA m 3 " BETA1-4 " 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 G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 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 h 2 " - " BMA h 3 " " 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 l 2 " - " BMA l 3 " " 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 p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 137 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 234 " " NAG B 603 " - " ASN B 301 " " NAG B 604 " - " ASN B 339 " " NAG B 605 " - " ASN B 355 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 137 " " NAG D 1 " - " ASN C 295 " " NAG E 1 " - " ASN C 386 " " NAG F 1 " - " ASN C 363 " " NAG G 1 " - " ASN C 160 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 392 " " NAG K 1 " - " ASN C 301 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 448 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN A 386 " " NAG V 1 " - " ASN A 392 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 197 " " NAG Z 1 " - " ASN A 332 " " NAG a 701 " - " ASN a 611 " " NAG a 702 " - " ASN a 637 " " NAG b 701 " - " ASN b 611 " " NAG b 702 " - " ASN b 637 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG d 1 " - " ASN B 332 " " NAG e 1 " - " ASN B 386 " " NAG f 1 " - " ASN B 363 " " NAG g 1 " - " ASN B 197 " " NAG h 1 " - " ASN B 160 " " NAG i 1 " - " ASN B 295 " " NAG j 1 " - " ASN B 133 " " NAG k 1 " - " ASN B 137 " " NAG l 1 " - " ASN B 156 " " NAG m 1 " - " ASN B 276 " " NAG n 1 " - " ASN B 392 " " NAG o 1 " - " ASN B 448 " " NAG p 1 " - " ASN C 262 " " NAG q 1 " - " ASN C 276 " " NAG r 1 " - " ASN B 262 " Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 2.6 seconds 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 23.3% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.531A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.623A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.510A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.998A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.979A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.630A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.650A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.722A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.608A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.462A pdb=" N GLY A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.065A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.289A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.328A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.557A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.608A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 537 through 542 Processing helix chain 'c' and resid 572 through 596 removed outlier: 4.048A pdb=" N LEU c 576 " --> pdb=" O GLY c 572 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL c 583 " --> pdb=" O ARG c 579 " (cutoff:3.500A) Processing helix chain 'c' and resid 611 through 615 Processing helix chain 'c' and resid 627 through 633 Processing helix chain 'c' and resid 634 through 635 No H-bonds generated for 'chain 'c' and resid 634 through 635' Processing helix chain 'c' and resid 636 through 637 No H-bonds generated for 'chain 'c' and resid 636 through 637' Processing helix chain 'c' and resid 638 through 664 removed outlier: 4.048A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN c 651 " --> pdb=" O GLU c 647 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN c 653 " --> pdb=" O SER c 649 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA c 662 " --> pdb=" O GLN c 658 " (cutoff:3.500A) Processing helix chain 'a' and resid 529 through 534 Processing helix chain 'a' and resid 536 through 542 removed outlier: 4.411A pdb=" N GLN a 540 " --> pdb=" O THR a 536 " (cutoff:3.500A) Processing helix chain 'a' and resid 569 through 571 No H-bonds generated for 'chain 'a' and resid 569 through 571' Processing helix chain 'a' and resid 572 through 595 removed outlier: 3.618A pdb=" N ARG a 588 " --> pdb=" O GLU a 584 " (cutoff:3.500A) Processing helix chain 'a' and resid 618 through 623 Processing helix chain 'a' and resid 627 through 635 removed outlier: 4.201A pdb=" N LYS a 633 " --> pdb=" O LEU a 629 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU a 634 " --> pdb=" O GLN a 630 " (cutoff:3.500A) Processing helix chain 'a' and resid 638 through 663 removed outlier: 3.693A pdb=" N GLY a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU a 647 " --> pdb=" O TYR a 643 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN a 652 " --> pdb=" O GLU a 648 " (cutoff:3.500A) Processing helix chain 'b' and resid 529 through 534 Processing helix chain 'b' and resid 536 through 542 removed outlier: 4.166A pdb=" N GLN b 540 " --> pdb=" O THR b 536 " (cutoff:3.500A) Processing helix chain 'b' and resid 570 through 596 removed outlier: 3.838A pdb=" N LYS b 574 " --> pdb=" O VAL b 570 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU b 576 " --> pdb=" O GLY b 572 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA b 578 " --> pdb=" O LYS b 574 " (cutoff:3.500A) Processing helix chain 'b' and resid 618 through 625 removed outlier: 3.839A pdb=" N ILE b 622 " --> pdb=" O ASN b 618 " (cutoff:3.500A) Processing helix chain 'b' and resid 627 through 636 removed outlier: 4.072A pdb=" N LYS b 633 " --> pdb=" O LEU b 629 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU b 634 " --> pdb=" O GLN b 630 " (cutoff:3.500A) Processing helix chain 'b' and resid 638 through 661 removed outlier: 3.515A pdb=" N GLU b 647 " --> pdb=" O TYR b 643 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU b 648 " --> pdb=" O GLY b 644 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN b 653 " --> pdb=" O SER b 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 5.798A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.388A pdb=" N VAL C 36 " --> pdb=" O THR c 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.061A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.030A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.575A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.253A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.190A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.586A pdb=" N ARG C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.190A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 421 removed outlier: 3.576A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.756A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.537A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL A 36 " --> pdb=" O THR a 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.758A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.728A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.642A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AB6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.507A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.804A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 413 through 418 removed outlier: 4.152A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.536A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AC3, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.687A pdb=" N VAL b 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL B 38 " --> pdb=" O THR b 606 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR b 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR B 40 " --> pdb=" O CYS b 604 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N CYS b 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.863A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.888A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.735A pdb=" N VAL B 120 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'B' and resid 271 through 273 removed outlier: 12.276A pdb=" N ILE B 284 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ASP B 457 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 457 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.700A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.700A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.574A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.650A pdb=" N CYS H 92 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP H 108 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR H 94 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS H 98 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU H 102 " --> pdb=" O HIS H 98 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU H 100 " --> pdb=" O ASP H 100R" (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP H 100R" --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP H 100B" --> pdb=" O TRP H 100P" (cutoff:3.500A) removed outlier: 7.239A pdb=" N TRP H 100P" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE H 100D" --> pdb=" O GLU H 100N" (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU H 100N" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.935A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.401A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG L 39 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS L 49 " --> pdb=" O HIS L 53 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1491 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: 6.41 Time building geometry restraints manager: 6.63 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: 5205 1.34 - 1.46: 4032 1.46 - 1.58: 8170 1.58 - 1.70: 2 1.70 - 1.82: 157 Bond restraints: 17566 Sorted by residual: bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.510 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" O3 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.458 1.509 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" O2 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.461 1.510 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.462 1.510 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.462 1.508 -0.046 2.00e-02 2.50e+03 5.33e+00 ... (remaining 17561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 23700 2.71 - 5.42: 141 5.42 - 8.12: 3 8.12 - 10.83: 3 10.83 - 13.54: 2 Bond angle restraints: 23849 Sorted by residual: angle pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" pdb=" O2 TYS H 100F" ideal model delta sigma weight residual 114.11 100.57 13.54 3.00e+00 1.11e-01 2.04e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O2 TYS H 100I" ideal model delta sigma weight residual 114.11 101.23 12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" OH TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 100.21 110.32 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OH TYS H 100F" pdb=" S TYS H 100F" pdb=" O3 TYS H 100F" ideal model delta sigma weight residual 100.21 109.58 -9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" OH TYS H 100F" pdb=" S TYS H 100F" pdb=" O2 TYS H 100F" ideal model delta sigma weight residual 104.74 114.11 -9.37 3.00e+00 1.11e-01 9.75e+00 ... (remaining 23844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 11489 16.66 - 33.32: 504 33.32 - 49.98: 151 49.98 - 66.64: 46 66.64 - 83.30: 6 Dihedral angle restraints: 12196 sinusoidal: 6513 harmonic: 5683 Sorted by residual: dihedral pdb=" CA ASN A 448 " pdb=" C ASN A 448 " pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.44 32.44 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -117.28 31.28 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 12193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2748 0.068 - 0.136: 294 0.136 - 0.203: 15 0.203 - 0.271: 3 0.271 - 0.339: 1 Chirality restraints: 3061 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 448 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG B 605 " pdb=" ND2 ASN B 355 " pdb=" C2 NAG B 605 " pdb=" O5 NAG B 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG o 1 " pdb=" ND2 ASN B 448 " pdb=" C2 NAG o 1 " pdb=" O5 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3058 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO B 212 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 42 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO C 43 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 298 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 299 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.017 5.00e-02 4.00e+02 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 131 2.56 - 3.14: 14312 3.14 - 3.73: 23788 3.73 - 4.31: 35302 4.31 - 4.90: 59742 Nonbonded interactions: 133275 Sorted by model distance: nonbonded pdb=" O ASP b 632 " pdb=" OG SER b 636 " model vdw 1.972 3.040 nonbonded pdb=" O THR C 278 " pdb=" O6 NAG q 1 " model vdw 2.058 3.040 nonbonded pdb=" OD2 ASP A 457 " pdb=" NH1 ARG A 469 " model vdw 2.113 3.120 nonbonded pdb=" NZ LYS C 169 " pdb=" OE2 GLU H 100N" model vdw 2.142 3.120 nonbonded pdb=" O THR A 278 " pdb=" O6 NAG X 1 " model vdw 2.144 3.040 ... (remaining 133270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 505 or resid 601 through 605)) selection = chain 'B' selection = (chain 'C' and (resid 33 through 397 or resid 411 through 505 or resid 601 throu \ gh 605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'G' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'm' selection = chain 'q' } ncs_group { reference = (chain 'P' and (resid 1 or resid 4 through 6)) selection = (chain 'R' and (resid 2 or resid 5 through 7)) selection = (chain 'p' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 1 or resid 4 through 6)) } ncs_group { reference = (chain 'a' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'b' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = chain 'c' } 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: 16.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.140 Find NCS groups from input model: 1.160 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17731 Z= 0.149 Angle : 0.640 13.541 24308 Z= 0.303 Chirality : 0.042 0.339 3061 Planarity : 0.003 0.052 2852 Dihedral : 10.404 83.301 8416 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.04 % Allowed : 3.92 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.19), residues: 1933 helix: -1.48 (0.25), residues: 373 sheet: -0.46 (0.24), residues: 466 loop : -0.95 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 69 HIS 0.004 0.001 HIS H 52A PHE 0.008 0.001 PHE A 93 TYR 0.008 0.001 TYR L 32 ARG 0.002 0.000 ARG a 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 60) link_NAG-ASN : angle 2.22153 ( 180) link_ALPHA1-6 : bond 0.01314 ( 6) link_ALPHA1-6 : angle 1.82150 ( 18) link_BETA1-4 : bond 0.00556 ( 49) link_BETA1-4 : angle 2.17598 ( 147) link_ALPHA1-2 : bond 0.01079 ( 4) link_ALPHA1-2 : angle 3.16460 ( 12) link_ALPHA1-3 : bond 0.01336 ( 9) link_ALPHA1-3 : angle 1.86874 ( 27) hydrogen bonds : bond 0.26026 ( 537) hydrogen bonds : angle 8.99831 ( 1491) SS BOND : bond 0.00183 ( 36) SS BOND : angle 0.88019 ( 72) link_BETA1-3 : bond 0.00830 ( 1) link_BETA1-3 : angle 3.93756 ( 3) covalent geometry : bond 0.00312 (17566) covalent geometry : angle 0.57911 (23849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 308 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7762 (mtm-85) REVERT: C 335 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7608 (tttt) REVERT: A 296 CYS cc_start: 0.8491 (m) cc_final: 0.7744 (m) REVERT: B 35 TRP cc_start: 0.8146 (m-90) cc_final: 0.7759 (m100) REVERT: B 69 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7407 (p90) REVERT: B 82 GLN cc_start: 0.8290 (mp10) cc_final: 0.7921 (mp10) REVERT: B 125 LEU cc_start: 0.9017 (tp) cc_final: 0.8702 (tp) REVERT: B 174 SER cc_start: 0.9006 (t) cc_final: 0.8701 (m) REVERT: B 207 LYS cc_start: 0.8548 (mttt) cc_final: 0.8341 (mtpp) REVERT: c 616 ASN cc_start: 0.7933 (t0) cc_final: 0.7506 (t0) REVERT: c 632 ASP cc_start: 0.8684 (t70) cc_final: 0.8389 (t0) REVERT: c 640 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7784 (tm-30) REVERT: c 653 GLN cc_start: 0.7877 (tp40) cc_final: 0.7315 (mt0) REVERT: c 658 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7774 (tm-30) REVERT: a 601 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8748 (mtmm) REVERT: b 655 LYS cc_start: 0.7972 (tptp) cc_final: 0.7544 (ttpp) REVERT: H 59 GLN cc_start: 0.7729 (tp40) cc_final: 0.6811 (pp30) REVERT: H 60 LYS cc_start: 0.8070 (tptp) cc_final: 0.7731 (tttp) REVERT: H 101 TYR cc_start: 0.8433 (m-80) cc_final: 0.7979 (m-80) REVERT: L 46 LEU cc_start: 0.8276 (pt) cc_final: 0.7965 (pp) outliers start: 18 outliers final: 8 residues processed: 289 average time/residue: 0.3764 time to fit residues: 157.6012 Evaluate side-chains 179 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 GLN A 33 ASN A 67 ASN A 103 GLN A 249 HIS B 249 HIS B 330 HIS B 428 GLN c 630 GLN c 640 GLN a 543 ASN b 653 GLN L 53 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.159619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122171 restraints weight = 23767.184| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.00 r_work: 0.3513 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17731 Z= 0.163 Angle : 0.734 10.783 24308 Z= 0.341 Chirality : 0.048 0.367 3061 Planarity : 0.004 0.042 2852 Dihedral : 8.348 59.645 4763 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.84 % Allowed : 8.18 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1933 helix: -0.50 (0.26), residues: 392 sheet: -0.38 (0.22), residues: 522 loop : -0.68 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.007 0.001 HIS L 93 PHE 0.011 0.002 PHE A 383 TYR 0.022 0.001 TYR c 638 ARG 0.005 0.001 ARG c 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 60) link_NAG-ASN : angle 2.77870 ( 180) link_ALPHA1-6 : bond 0.00753 ( 6) link_ALPHA1-6 : angle 1.50503 ( 18) link_BETA1-4 : bond 0.00513 ( 49) link_BETA1-4 : angle 2.02351 ( 147) link_ALPHA1-2 : bond 0.00541 ( 4) link_ALPHA1-2 : angle 2.22671 ( 12) link_ALPHA1-3 : bond 0.01128 ( 9) link_ALPHA1-3 : angle 1.83255 ( 27) hydrogen bonds : bond 0.05723 ( 537) hydrogen bonds : angle 5.83562 ( 1491) SS BOND : bond 0.00229 ( 36) SS BOND : angle 1.36794 ( 72) link_BETA1-3 : bond 0.01203 ( 1) link_BETA1-3 : angle 4.21403 ( 3) covalent geometry : bond 0.00363 (17566) covalent geometry : angle 0.67026 (23849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.7979 (tpp) cc_final: 0.7609 (tpp) REVERT: C 308 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7844 (mtm-85) REVERT: A 209 SER cc_start: 0.8764 (t) cc_final: 0.8414 (p) REVERT: B 35 TRP cc_start: 0.8281 (m-90) cc_final: 0.7989 (m100) REVERT: B 69 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.7646 (p90) REVERT: B 82 GLN cc_start: 0.8270 (mp10) cc_final: 0.8042 (mp10) REVERT: B 125 LEU cc_start: 0.9021 (tp) cc_final: 0.8764 (tp) REVERT: B 207 LYS cc_start: 0.8674 (mttt) cc_final: 0.8450 (mtpp) REVERT: c 616 ASN cc_start: 0.7631 (t0) cc_final: 0.7246 (t0) REVERT: c 630 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: c 632 ASP cc_start: 0.8483 (t70) cc_final: 0.8171 (t0) REVERT: c 635 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8334 (mm) REVERT: c 653 GLN cc_start: 0.8094 (tp40) cc_final: 0.7668 (mt0) REVERT: c 658 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8118 (tm-30) REVERT: a 601 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8729 (mtmm) REVERT: a 634 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8209 (mt-10) REVERT: b 655 LYS cc_start: 0.8088 (tptp) cc_final: 0.7667 (ttpp) REVERT: H 52 GLU cc_start: 0.7979 (mp0) cc_final: 0.7686 (mp0) REVERT: H 59 GLN cc_start: 0.7654 (tp40) cc_final: 0.6801 (pp30) REVERT: H 60 LYS cc_start: 0.8035 (tptp) cc_final: 0.7731 (tttp) REVERT: H 93 LEU cc_start: 0.7271 (pp) cc_final: 0.7060 (pp) REVERT: H 101 TYR cc_start: 0.8595 (m-80) cc_final: 0.8178 (m-80) REVERT: L 46 LEU cc_start: 0.8297 (pt) cc_final: 0.7970 (pp) REVERT: L 93 HIS cc_start: 0.6156 (m-70) cc_final: 0.5855 (m-70) outliers start: 32 outliers final: 16 residues processed: 215 average time/residue: 0.2958 time to fit residues: 96.9813 Evaluate side-chains 185 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 630 GLN Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain b residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN c 625 ASN c 630 GLN a 543 ASN H 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.150454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110665 restraints weight = 25379.346| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.16 r_work: 0.3277 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17731 Z= 0.202 Angle : 0.742 13.559 24308 Z= 0.340 Chirality : 0.049 0.367 3061 Planarity : 0.004 0.041 2852 Dihedral : 8.519 59.495 4759 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.42 % Allowed : 9.80 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1933 helix: -0.35 (0.26), residues: 403 sheet: -0.43 (0.22), residues: 514 loop : -0.73 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 PHE 0.014 0.002 PHE B 317 TYR 0.029 0.002 TYR H 79 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 60) link_NAG-ASN : angle 3.04715 ( 180) link_ALPHA1-6 : bond 0.00665 ( 6) link_ALPHA1-6 : angle 1.58591 ( 18) link_BETA1-4 : bond 0.00557 ( 49) link_BETA1-4 : angle 1.99258 ( 147) link_ALPHA1-2 : bond 0.00447 ( 4) link_ALPHA1-2 : angle 2.24828 ( 12) link_ALPHA1-3 : bond 0.01079 ( 9) link_ALPHA1-3 : angle 1.74165 ( 27) hydrogen bonds : bond 0.05254 ( 537) hydrogen bonds : angle 5.51310 ( 1491) SS BOND : bond 0.00273 ( 36) SS BOND : angle 1.62560 ( 72) link_BETA1-3 : bond 0.01206 ( 1) link_BETA1-3 : angle 3.96798 ( 3) covalent geometry : bond 0.00476 (17566) covalent geometry : angle 0.67041 (23849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8576 (tt0) cc_final: 0.7973 (tt0) REVERT: C 246 GLN cc_start: 0.7512 (mt0) cc_final: 0.7235 (tp40) REVERT: A 192 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7690 (ptt-90) REVERT: A 209 SER cc_start: 0.8794 (t) cc_final: 0.8340 (p) REVERT: B 35 TRP cc_start: 0.8293 (m-90) cc_final: 0.7944 (m100) REVERT: B 69 TRP cc_start: 0.7804 (OUTLIER) cc_final: 0.7300 (p90) REVERT: B 125 LEU cc_start: 0.9148 (tp) cc_final: 0.8757 (tp) REVERT: B 174 SER cc_start: 0.9028 (t) cc_final: 0.8752 (m) REVERT: B 207 LYS cc_start: 0.8603 (mttt) cc_final: 0.8332 (mtpp) REVERT: c 616 ASN cc_start: 0.7654 (t0) cc_final: 0.7289 (t0) REVERT: c 632 ASP cc_start: 0.8520 (t70) cc_final: 0.8205 (t0) REVERT: c 653 GLN cc_start: 0.8021 (tp40) cc_final: 0.7637 (mt0) REVERT: c 658 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7806 (tm-30) REVERT: a 601 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8698 (mtmm) REVERT: a 634 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8245 (mt-10) REVERT: b 637 ASN cc_start: 0.7493 (m-40) cc_final: 0.7160 (m-40) REVERT: b 655 LYS cc_start: 0.8216 (tptp) cc_final: 0.7705 (ttpp) REVERT: H 52 GLU cc_start: 0.8105 (mp0) cc_final: 0.7832 (mp0) REVERT: H 59 GLN cc_start: 0.7691 (tp40) cc_final: 0.6861 (pp30) REVERT: H 60 LYS cc_start: 0.7998 (tptp) cc_final: 0.7663 (tttp) REVERT: H 101 TYR cc_start: 0.8577 (m-80) cc_final: 0.8240 (m-80) REVERT: L 46 LEU cc_start: 0.8386 (pt) cc_final: 0.8139 (pp) outliers start: 42 outliers final: 30 residues processed: 210 average time/residue: 0.3151 time to fit residues: 100.6023 Evaluate side-chains 205 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN A 103 GLN B 183 GLN B 330 HIS c 625 ASN c 630 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110868 restraints weight = 25514.276| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.18 r_work: 0.3280 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17731 Z= 0.167 Angle : 0.692 10.999 24308 Z= 0.315 Chirality : 0.047 0.376 3061 Planarity : 0.004 0.041 2852 Dihedral : 8.547 59.423 4759 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.77 % Allowed : 10.72 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1933 helix: -0.12 (0.27), residues: 402 sheet: -0.34 (0.22), residues: 531 loop : -0.71 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 PHE 0.011 0.001 PHE B 317 TYR 0.022 0.001 TYR H 79 ARG 0.005 0.000 ARG b 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 60) link_NAG-ASN : angle 2.86730 ( 180) link_ALPHA1-6 : bond 0.00702 ( 6) link_ALPHA1-6 : angle 1.54143 ( 18) link_BETA1-4 : bond 0.00519 ( 49) link_BETA1-4 : angle 1.88504 ( 147) link_ALPHA1-2 : bond 0.00427 ( 4) link_ALPHA1-2 : angle 2.09587 ( 12) link_ALPHA1-3 : bond 0.01101 ( 9) link_ALPHA1-3 : angle 1.73866 ( 27) hydrogen bonds : bond 0.04457 ( 537) hydrogen bonds : angle 5.17151 ( 1491) SS BOND : bond 0.00381 ( 36) SS BOND : angle 1.25883 ( 72) link_BETA1-3 : bond 0.01166 ( 1) link_BETA1-3 : angle 3.73336 ( 3) covalent geometry : bond 0.00388 (17566) covalent geometry : angle 0.62475 (23849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8555 (tt0) cc_final: 0.7944 (tt0) REVERT: C 161 MET cc_start: 0.8199 (tpp) cc_final: 0.7762 (ttm) REVERT: C 246 GLN cc_start: 0.7573 (mt0) cc_final: 0.7297 (tp40) REVERT: A 192 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7658 (ptt-90) REVERT: A 207 LYS cc_start: 0.8340 (tptt) cc_final: 0.8104 (tptt) REVERT: A 209 SER cc_start: 0.8761 (t) cc_final: 0.8392 (p) REVERT: B 35 TRP cc_start: 0.8301 (m-90) cc_final: 0.7970 (m100) REVERT: B 69 TRP cc_start: 0.7816 (OUTLIER) cc_final: 0.6988 (p90) REVERT: B 125 LEU cc_start: 0.9135 (tp) cc_final: 0.8740 (tp) REVERT: B 174 SER cc_start: 0.8999 (t) cc_final: 0.8722 (m) REVERT: B 207 LYS cc_start: 0.8651 (mttt) cc_final: 0.8405 (mtpp) REVERT: c 616 ASN cc_start: 0.7528 (t0) cc_final: 0.7148 (t0) REVERT: c 632 ASP cc_start: 0.8533 (t70) cc_final: 0.8281 (t0) REVERT: c 635 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7810 (mm) REVERT: c 653 GLN cc_start: 0.8133 (tp40) cc_final: 0.7723 (mt0) REVERT: a 588 ARG cc_start: 0.8080 (ttp-170) cc_final: 0.7729 (ttm110) REVERT: a 601 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8672 (mtmm) REVERT: a 634 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8171 (mt-10) REVERT: b 632 ASP cc_start: 0.8003 (p0) cc_final: 0.7774 (p0) REVERT: b 637 ASN cc_start: 0.7348 (m-40) cc_final: 0.7048 (m-40) REVERT: b 655 LYS cc_start: 0.8122 (tptp) cc_final: 0.7709 (ttpp) REVERT: H 52 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: H 59 GLN cc_start: 0.7704 (tp40) cc_final: 0.6887 (pp30) REVERT: H 60 LYS cc_start: 0.7976 (tptp) cc_final: 0.7652 (tttp) REVERT: H 101 TYR cc_start: 0.8567 (m-80) cc_final: 0.8221 (m-80) REVERT: L 46 LEU cc_start: 0.8428 (pt) cc_final: 0.8210 (pp) REVERT: L 96 TRP cc_start: 0.7729 (m-90) cc_final: 0.6890 (m-90) outliers start: 48 outliers final: 31 residues processed: 210 average time/residue: 0.3012 time to fit residues: 96.7503 Evaluate side-chains 201 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain b residue 636 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 167 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 140 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109922 restraints weight = 26135.616| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.18 r_work: 0.3224 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17731 Z= 0.222 Angle : 0.736 11.428 24308 Z= 0.335 Chirality : 0.049 0.384 3061 Planarity : 0.004 0.042 2852 Dihedral : 8.732 59.646 4759 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.11 % Allowed : 11.70 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1933 helix: -0.16 (0.27), residues: 400 sheet: -0.59 (0.21), residues: 569 loop : -0.71 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 112 HIS 0.006 0.002 HIS B 330 PHE 0.016 0.002 PHE B 53 TYR 0.020 0.002 TYR a 638 ARG 0.005 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 60) link_NAG-ASN : angle 2.89467 ( 180) link_ALPHA1-6 : bond 0.00621 ( 6) link_ALPHA1-6 : angle 1.60135 ( 18) link_BETA1-4 : bond 0.00531 ( 49) link_BETA1-4 : angle 1.90663 ( 147) link_ALPHA1-2 : bond 0.00425 ( 4) link_ALPHA1-2 : angle 2.08740 ( 12) link_ALPHA1-3 : bond 0.01029 ( 9) link_ALPHA1-3 : angle 1.72504 ( 27) hydrogen bonds : bond 0.04635 ( 537) hydrogen bonds : angle 5.21490 ( 1491) SS BOND : bond 0.00328 ( 36) SS BOND : angle 1.55102 ( 72) link_BETA1-3 : bond 0.01216 ( 1) link_BETA1-3 : angle 3.57383 ( 3) covalent geometry : bond 0.00530 (17566) covalent geometry : angle 0.67112 (23849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8610 (tt0) cc_final: 0.7993 (tt0) REVERT: C 246 GLN cc_start: 0.7662 (mt0) cc_final: 0.7334 (tp40) REVERT: A 192 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7711 (ptt-90) REVERT: A 209 SER cc_start: 0.8816 (t) cc_final: 0.8386 (p) REVERT: A 330 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8232 (p90) REVERT: B 35 TRP cc_start: 0.8326 (m-90) cc_final: 0.7966 (m100) REVERT: B 125 LEU cc_start: 0.9203 (tp) cc_final: 0.8747 (tp) REVERT: B 174 SER cc_start: 0.9023 (t) cc_final: 0.8742 (m) REVERT: B 207 LYS cc_start: 0.8681 (mttt) cc_final: 0.8441 (mtpp) REVERT: c 616 ASN cc_start: 0.7626 (t0) cc_final: 0.7245 (t0) REVERT: c 632 ASP cc_start: 0.8626 (t70) cc_final: 0.8343 (t0) REVERT: c 635 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7815 (mm) REVERT: c 653 GLN cc_start: 0.8164 (tp40) cc_final: 0.7719 (mt0) REVERT: a 588 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7728 (ttm110) REVERT: a 601 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8686 (mtmm) REVERT: a 634 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8227 (mt-10) REVERT: b 638 TYR cc_start: 0.7497 (m-80) cc_final: 0.7266 (m-80) REVERT: b 655 LYS cc_start: 0.8169 (tptp) cc_final: 0.7685 (ttpp) REVERT: H 52 GLU cc_start: 0.8247 (mp0) cc_final: 0.7942 (mp0) REVERT: H 59 GLN cc_start: 0.7724 (tp40) cc_final: 0.6857 (pp30) REVERT: H 60 LYS cc_start: 0.8033 (tptp) cc_final: 0.7694 (tttp) REVERT: H 101 TYR cc_start: 0.8622 (m-80) cc_final: 0.8218 (m-80) REVERT: H 104 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8302 (t) REVERT: L 46 LEU cc_start: 0.8369 (pt) cc_final: 0.8133 (pp) REVERT: L 96 TRP cc_start: 0.7779 (m-90) cc_final: 0.6951 (m-90) outliers start: 54 outliers final: 41 residues processed: 216 average time/residue: 0.2954 time to fit residues: 96.6363 Evaluate side-chains 216 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 636 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 82 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110982 restraints weight = 25746.843| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.80 r_work: 0.3276 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17731 Z= 0.147 Angle : 0.683 11.330 24308 Z= 0.308 Chirality : 0.047 0.373 3061 Planarity : 0.004 0.045 2852 Dihedral : 8.510 63.660 4759 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.11 % Allowed : 12.16 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1933 helix: -0.01 (0.27), residues: 406 sheet: -0.34 (0.22), residues: 529 loop : -0.72 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 112 HIS 0.005 0.001 HIS A 249 PHE 0.014 0.001 PHE B 53 TYR 0.020 0.001 TYR a 638 ARG 0.006 0.000 ARG b 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 60) link_NAG-ASN : angle 2.84125 ( 180) link_ALPHA1-6 : bond 0.00703 ( 6) link_ALPHA1-6 : angle 1.53186 ( 18) link_BETA1-4 : bond 0.00502 ( 49) link_BETA1-4 : angle 1.83342 ( 147) link_ALPHA1-2 : bond 0.00430 ( 4) link_ALPHA1-2 : angle 1.95865 ( 12) link_ALPHA1-3 : bond 0.01064 ( 9) link_ALPHA1-3 : angle 1.70525 ( 27) hydrogen bonds : bond 0.04148 ( 537) hydrogen bonds : angle 4.95598 ( 1491) SS BOND : bond 0.00239 ( 36) SS BOND : angle 1.17395 ( 72) link_BETA1-3 : bond 0.01152 ( 1) link_BETA1-3 : angle 3.41619 ( 3) covalent geometry : bond 0.00337 (17566) covalent geometry : angle 0.61748 (23849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8543 (tt0) cc_final: 0.7924 (tt0) REVERT: C 246 GLN cc_start: 0.7644 (mt0) cc_final: 0.7336 (tp40) REVERT: A 192 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7673 (ptt-90) REVERT: A 209 SER cc_start: 0.8788 (t) cc_final: 0.8382 (p) REVERT: B 35 TRP cc_start: 0.8308 (m-90) cc_final: 0.7950 (m100) REVERT: B 125 LEU cc_start: 0.9119 (tp) cc_final: 0.8701 (tp) REVERT: B 174 SER cc_start: 0.8998 (t) cc_final: 0.8718 (m) REVERT: B 207 LYS cc_start: 0.8695 (mttt) cc_final: 0.8477 (mtpp) REVERT: B 368 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7656 (p0) REVERT: c 616 ASN cc_start: 0.7540 (t0) cc_final: 0.7157 (t0) REVERT: c 632 ASP cc_start: 0.8522 (t70) cc_final: 0.8249 (t0) REVERT: c 635 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7645 (mm) REVERT: c 653 GLN cc_start: 0.8105 (tp40) cc_final: 0.7685 (mt0) REVERT: c 658 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7544 (tp40) REVERT: a 588 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7687 (ttm110) REVERT: a 601 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8773 (mtmm) REVERT: a 634 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8164 (mt-10) REVERT: b 655 LYS cc_start: 0.8164 (tptp) cc_final: 0.7701 (ttpp) REVERT: H 52 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: H 60 LYS cc_start: 0.7998 (tptp) cc_final: 0.7654 (tttp) REVERT: H 101 TYR cc_start: 0.8568 (m-80) cc_final: 0.8223 (m-80) REVERT: H 104 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8324 (t) REVERT: L 46 LEU cc_start: 0.8396 (pt) cc_final: 0.8174 (pp) REVERT: L 96 TRP cc_start: 0.7728 (m-90) cc_final: 0.7026 (m-90) outliers start: 54 outliers final: 37 residues processed: 212 average time/residue: 0.2901 time to fit residues: 94.1044 Evaluate side-chains 205 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.150956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111478 restraints weight = 25623.948| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.19 r_work: 0.3293 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17731 Z= 0.139 Angle : 0.674 11.526 24308 Z= 0.305 Chirality : 0.046 0.373 3061 Planarity : 0.003 0.047 2852 Dihedral : 8.315 59.399 4755 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.11 % Allowed : 12.56 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1933 helix: 0.13 (0.27), residues: 403 sheet: -0.38 (0.21), residues: 543 loop : -0.65 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE B 53 TYR 0.022 0.001 TYR a 638 ARG 0.006 0.000 ARG b 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 60) link_NAG-ASN : angle 2.70908 ( 180) link_ALPHA1-6 : bond 0.00695 ( 6) link_ALPHA1-6 : angle 1.52516 ( 18) link_BETA1-4 : bond 0.00534 ( 49) link_BETA1-4 : angle 1.82316 ( 147) link_ALPHA1-2 : bond 0.00412 ( 4) link_ALPHA1-2 : angle 1.89933 ( 12) link_ALPHA1-3 : bond 0.01036 ( 9) link_ALPHA1-3 : angle 1.69421 ( 27) hydrogen bonds : bond 0.03969 ( 537) hydrogen bonds : angle 4.84158 ( 1491) SS BOND : bond 0.00221 ( 36) SS BOND : angle 1.32356 ( 72) link_BETA1-3 : bond 0.01143 ( 1) link_BETA1-3 : angle 3.32121 ( 3) covalent geometry : bond 0.00317 (17566) covalent geometry : angle 0.61081 (23849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7650 (mt0) cc_final: 0.7366 (tp40) REVERT: C 356 ASN cc_start: 0.8240 (t0) cc_final: 0.8007 (t0) REVERT: A 192 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7658 (ptt-90) REVERT: A 207 LYS cc_start: 0.8235 (tptt) cc_final: 0.7814 (tptt) REVERT: A 209 SER cc_start: 0.8769 (t) cc_final: 0.8377 (p) REVERT: B 35 TRP cc_start: 0.8325 (m-90) cc_final: 0.7930 (m100) REVERT: B 125 LEU cc_start: 0.9089 (tp) cc_final: 0.8654 (tp) REVERT: B 207 LYS cc_start: 0.8718 (mttt) cc_final: 0.8486 (mtpp) REVERT: B 368 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7652 (p0) REVERT: c 616 ASN cc_start: 0.7451 (t0) cc_final: 0.7083 (t0) REVERT: c 632 ASP cc_start: 0.8457 (t70) cc_final: 0.8206 (t0) REVERT: c 635 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7601 (mm) REVERT: c 653 GLN cc_start: 0.8152 (tp40) cc_final: 0.7784 (mt0) REVERT: c 658 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7791 (tp40) REVERT: a 588 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7681 (ttm110) REVERT: a 601 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8806 (mtmm) REVERT: a 634 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8136 (mt-10) REVERT: b 655 LYS cc_start: 0.8160 (tptp) cc_final: 0.7696 (ttpp) REVERT: H 52 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: H 101 TYR cc_start: 0.8584 (m-80) cc_final: 0.8241 (m-80) REVERT: H 104 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8328 (t) REVERT: L 46 LEU cc_start: 0.8386 (pt) cc_final: 0.8170 (pp) REVERT: L 96 TRP cc_start: 0.7777 (m-90) cc_final: 0.7089 (m-90) outliers start: 54 outliers final: 42 residues processed: 216 average time/residue: 0.2888 time to fit residues: 94.7361 Evaluate side-chains 211 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52AHIS ** L 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109396 restraints weight = 25548.310| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.11 r_work: 0.3309 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17731 Z= 0.219 Angle : 0.734 11.819 24308 Z= 0.335 Chirality : 0.048 0.383 3061 Planarity : 0.004 0.052 2852 Dihedral : 8.624 59.763 4755 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.05 % Allowed : 12.91 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1933 helix: -0.07 (0.27), residues: 410 sheet: -0.47 (0.21), residues: 551 loop : -0.68 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 112 HIS 0.007 0.001 HIS L 93 PHE 0.014 0.002 PHE B 317 TYR 0.023 0.002 TYR a 638 ARG 0.006 0.000 ARG b 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 60) link_NAG-ASN : angle 2.81665 ( 180) link_ALPHA1-6 : bond 0.00629 ( 6) link_ALPHA1-6 : angle 1.59389 ( 18) link_BETA1-4 : bond 0.00520 ( 49) link_BETA1-4 : angle 1.83742 ( 147) link_ALPHA1-2 : bond 0.00399 ( 4) link_ALPHA1-2 : angle 1.97596 ( 12) link_ALPHA1-3 : bond 0.00997 ( 9) link_ALPHA1-3 : angle 1.69470 ( 27) hydrogen bonds : bond 0.04419 ( 537) hydrogen bonds : angle 5.05098 ( 1491) SS BOND : bond 0.00275 ( 36) SS BOND : angle 1.48298 ( 72) link_BETA1-3 : bond 0.01218 ( 1) link_BETA1-3 : angle 3.21466 ( 3) covalent geometry : bond 0.00521 (17566) covalent geometry : angle 0.67323 (23849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7993 (mt0) cc_final: 0.7529 (tp40) REVERT: A 192 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7806 (ptt-90) REVERT: A 207 LYS cc_start: 0.8304 (tptt) cc_final: 0.8042 (tptp) REVERT: A 209 SER cc_start: 0.8849 (t) cc_final: 0.8435 (p) REVERT: B 35 TRP cc_start: 0.8484 (m-90) cc_final: 0.8101 (m100) REVERT: B 125 LEU cc_start: 0.9173 (tp) cc_final: 0.8694 (tp) REVERT: B 207 LYS cc_start: 0.8756 (mttt) cc_final: 0.8516 (mtpp) REVERT: B 368 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7672 (p0) REVERT: c 616 ASN cc_start: 0.7682 (t0) cc_final: 0.7326 (t0) REVERT: c 632 ASP cc_start: 0.8597 (t70) cc_final: 0.8342 (t0) REVERT: c 635 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7586 (mm) REVERT: c 653 GLN cc_start: 0.8280 (tp40) cc_final: 0.7826 (mt0) REVERT: c 658 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7778 (tp40) REVERT: a 601 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8767 (mtmm) REVERT: a 634 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8234 (mt-10) REVERT: b 655 LYS cc_start: 0.8216 (tptp) cc_final: 0.7686 (ttpp) REVERT: H 101 TYR cc_start: 0.8770 (m-80) cc_final: 0.8554 (m-80) REVERT: H 104 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8424 (t) REVERT: L 46 LEU cc_start: 0.8369 (pt) cc_final: 0.8141 (pp) REVERT: L 96 TRP cc_start: 0.7993 (m-90) cc_final: 0.7198 (m-90) outliers start: 53 outliers final: 46 residues processed: 210 average time/residue: 0.3126 time to fit residues: 99.5915 Evaluate side-chains 211 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 636 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 161 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.151072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111874 restraints weight = 25681.191| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.13 r_work: 0.3296 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17731 Z= 0.127 Angle : 0.666 12.738 24308 Z= 0.301 Chirality : 0.046 0.371 3061 Planarity : 0.003 0.048 2852 Dihedral : 8.300 59.973 4755 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.05 % Allowed : 12.97 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1933 helix: 0.32 (0.27), residues: 398 sheet: -0.24 (0.22), residues: 524 loop : -0.69 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.007 0.001 HIS L 93 PHE 0.015 0.001 PHE H 61 TYR 0.020 0.001 TYR a 638 ARG 0.006 0.000 ARG b 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 60) link_NAG-ASN : angle 2.70429 ( 180) link_ALPHA1-6 : bond 0.00714 ( 6) link_ALPHA1-6 : angle 1.50267 ( 18) link_BETA1-4 : bond 0.00501 ( 49) link_BETA1-4 : angle 1.76695 ( 147) link_ALPHA1-2 : bond 0.00403 ( 4) link_ALPHA1-2 : angle 1.84261 ( 12) link_ALPHA1-3 : bond 0.01048 ( 9) link_ALPHA1-3 : angle 1.69286 ( 27) hydrogen bonds : bond 0.03855 ( 537) hydrogen bonds : angle 4.80588 ( 1491) SS BOND : bond 0.00223 ( 36) SS BOND : angle 1.19933 ( 72) link_BETA1-3 : bond 0.01128 ( 1) link_BETA1-3 : angle 3.10722 ( 3) covalent geometry : bond 0.00287 (17566) covalent geometry : angle 0.60401 (23849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7767 (mt0) cc_final: 0.7492 (tp40) REVERT: A 192 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7660 (ptt-90) REVERT: A 195 ASN cc_start: 0.8814 (p0) cc_final: 0.8559 (p0) REVERT: A 207 LYS cc_start: 0.8267 (tptt) cc_final: 0.7795 (tptt) REVERT: B 35 TRP cc_start: 0.8331 (m-90) cc_final: 0.7917 (m100) REVERT: B 125 LEU cc_start: 0.9068 (tp) cc_final: 0.8645 (tp) REVERT: B 207 LYS cc_start: 0.8689 (mttt) cc_final: 0.8475 (mtpp) REVERT: B 368 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7617 (p0) REVERT: c 616 ASN cc_start: 0.7465 (t0) cc_final: 0.7109 (t0) REVERT: c 632 ASP cc_start: 0.8480 (t70) cc_final: 0.8235 (t0) REVERT: c 635 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7364 (mm) REVERT: c 653 GLN cc_start: 0.8135 (tp40) cc_final: 0.7799 (mt0) REVERT: c 658 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7616 (tp40) REVERT: a 601 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8772 (mtmm) REVERT: a 634 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8138 (mt-10) REVERT: b 655 LYS cc_start: 0.8151 (tptp) cc_final: 0.7704 (ttpp) REVERT: H 52 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: H 101 TYR cc_start: 0.8553 (m-80) cc_final: 0.8155 (m-80) REVERT: H 104 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8332 (t) REVERT: L 46 LEU cc_start: 0.8346 (pt) cc_final: 0.8112 (pp) REVERT: L 96 TRP cc_start: 0.7812 (m-90) cc_final: 0.7169 (m-90) outliers start: 53 outliers final: 44 residues processed: 218 average time/residue: 0.3469 time to fit residues: 117.0750 Evaluate side-chains 215 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 636 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9980 chunk 68 optimal weight: 0.0870 chunk 92 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 0.0060 chunk 193 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113649 restraints weight = 25451.736| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.14 r_work: 0.3324 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17731 Z= 0.111 Angle : 0.653 11.277 24308 Z= 0.298 Chirality : 0.045 0.362 3061 Planarity : 0.003 0.047 2852 Dihedral : 8.031 59.603 4755 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.65 % Allowed : 13.72 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1933 helix: 0.78 (0.28), residues: 380 sheet: -0.18 (0.22), residues: 510 loop : -0.56 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS H 35 PHE 0.022 0.001 PHE H 61 TYR 0.020 0.001 TYR a 638 ARG 0.006 0.000 ARG b 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 60) link_NAG-ASN : angle 2.58479 ( 180) link_ALPHA1-6 : bond 0.00748 ( 6) link_ALPHA1-6 : angle 1.46525 ( 18) link_BETA1-4 : bond 0.00551 ( 49) link_BETA1-4 : angle 1.75613 ( 147) link_ALPHA1-2 : bond 0.00429 ( 4) link_ALPHA1-2 : angle 1.74074 ( 12) link_ALPHA1-3 : bond 0.01023 ( 9) link_ALPHA1-3 : angle 1.69257 ( 27) hydrogen bonds : bond 0.03542 ( 537) hydrogen bonds : angle 4.61786 ( 1491) SS BOND : bond 0.00248 ( 36) SS BOND : angle 1.22127 ( 72) link_BETA1-3 : bond 0.01089 ( 1) link_BETA1-3 : angle 3.07886 ( 3) covalent geometry : bond 0.00237 (17566) covalent geometry : angle 0.59452 (23849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7752 (mt0) cc_final: 0.7486 (tp40) REVERT: A 192 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7598 (ptt-90) REVERT: A 195 ASN cc_start: 0.8803 (p0) cc_final: 0.8501 (p0) REVERT: A 207 LYS cc_start: 0.8185 (tptt) cc_final: 0.7710 (tptt) REVERT: B 35 TRP cc_start: 0.8314 (m-90) cc_final: 0.7880 (m100) REVERT: B 125 LEU cc_start: 0.9010 (tp) cc_final: 0.8621 (tp) REVERT: B 207 LYS cc_start: 0.8730 (mttt) cc_final: 0.8472 (mtpp) REVERT: c 616 ASN cc_start: 0.7388 (t0) cc_final: 0.7044 (t0) REVERT: c 635 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7361 (mm) REVERT: c 653 GLN cc_start: 0.8109 (tp40) cc_final: 0.7864 (mt0) REVERT: a 601 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8747 (mtmm) REVERT: a 634 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8077 (mt-10) REVERT: b 655 LYS cc_start: 0.8094 (tptp) cc_final: 0.7691 (ttpp) REVERT: H 104 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8350 (t) REVERT: L 46 LEU cc_start: 0.8313 (pt) cc_final: 0.8103 (pp) REVERT: L 96 TRP cc_start: 0.7698 (m-90) cc_final: 0.7242 (m-90) outliers start: 46 outliers final: 38 residues processed: 214 average time/residue: 0.3591 time to fit residues: 117.1776 Evaluate side-chains 208 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 70 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 42 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: C 280 ASN a 543 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112107 restraints weight = 25579.040| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.68 r_work: 0.3292 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17731 Z= 0.147 Angle : 0.677 11.335 24308 Z= 0.309 Chirality : 0.046 0.369 3061 Planarity : 0.004 0.052 2852 Dihedral : 8.091 59.654 4751 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.88 % Allowed : 13.60 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1933 helix: 0.87 (0.28), residues: 373 sheet: -0.17 (0.22), residues: 518 loop : -0.61 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 112 HIS 0.007 0.001 HIS H 35 PHE 0.011 0.001 PHE B 53 TYR 0.022 0.001 TYR a 638 ARG 0.007 0.000 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 60) link_NAG-ASN : angle 2.52224 ( 180) link_ALPHA1-6 : bond 0.00710 ( 6) link_ALPHA1-6 : angle 1.50953 ( 18) link_BETA1-4 : bond 0.00538 ( 49) link_BETA1-4 : angle 1.77043 ( 147) link_ALPHA1-2 : bond 0.00393 ( 4) link_ALPHA1-2 : angle 1.77532 ( 12) link_ALPHA1-3 : bond 0.00982 ( 9) link_ALPHA1-3 : angle 1.68061 ( 27) hydrogen bonds : bond 0.03764 ( 537) hydrogen bonds : angle 4.65034 ( 1491) SS BOND : bond 0.00223 ( 36) SS BOND : angle 1.36913 ( 72) link_BETA1-3 : bond 0.01144 ( 1) link_BETA1-3 : angle 3.05483 ( 3) covalent geometry : bond 0.00340 (17566) covalent geometry : angle 0.62204 (23849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8296.64 seconds wall clock time: 145 minutes 58.97 seconds (8758.97 seconds total)