Starting phenix.real_space_refine on Tue Jun 17 21:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ulc_20813/06_2025/6ulc_20813_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ulc_20813/06_2025/6ulc_20813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ulc_20813/06_2025/6ulc_20813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ulc_20813/06_2025/6ulc_20813.map" model { file = "/net/cci-nas-00/data/ceres_data/6ulc_20813/06_2025/6ulc_20813_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ulc_20813/06_2025/6ulc_20813_neut.cif" } resolution = 4.6 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12400 2.51 5 N 3272 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 19968 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "F" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "H" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1836 Classifications: {'peptide': 240} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 227} Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1593 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3} 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: "I" 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: "J" 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: "K" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "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: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" 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: "e" 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: "f" 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: "g" 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" 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: "k" 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "n" 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: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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 Time building chain proxies: 10.97, per 1000 atoms: 0.55 Number of scatterers: 19968 At special positions: 0 Unit cell: (139.4, 195.16, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4184 8.00 N 3272 7.00 C 12400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " 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 296 " - pdb=" SG CYS A 331 " distance=1.91 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 385 " distance=1.92 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 418 " distance=2.28 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.27 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=1.83 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=1.92 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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 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=1.90 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 385 " distance=1.92 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 418 " distance=2.28 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 385 " distance=2.26 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 418 " distance=1.82 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.05 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=1.92 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.91 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 385 " distance=1.90 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 418 " distance=2.29 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 385 " distance=2.27 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 418 " distance=1.84 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=1.91 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 193 " 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=3, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA a 3 " - " MAN a 7 " " MAN a 4 " - " MAN a 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 6 " BETA1-2 " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG G 5 " - " GAL G 6 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG m 1 " - " FUC m 4 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 608 " - " ASN A 138 " " NAG A 609 " - " ASN A 145 " " NAG A 615 " - " ASN A 188 " " NAG A 621 " - " ASN A 234 " " NAG A 622 " - " ASN A 241 " " NAG A 626 " - " ASN A 276 " " NAG A 627 " - " ASN A 289 " " NAG A 628 " - " ASN A 295 " " NAG A 629 " - " ASN A 301 " " NAG A 630 " - " ASN A 332 " " NAG A 631 " - " ASN A 355 " " NAG A 637 " - " ASN A 394 " " NAG A 638 " - " ASN A 398 " " NAG A 639 " - " ASN A 411 " " NAG A 640 " - " ASN A 448 " " NAG A 641 " - " ASN A 463 " " NAG B 903 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 134 " " NAG C 614 " - " ASN C 197 " " NAG C 615 " - " ASN C 234 " " NAG C 618 " - " ASN C 276 " " NAG C 619 " - " ASN C 289 " " NAG C 620 " - " ASN C 295 " " NAG C 621 " - " ASN C 301 " " NAG C 622 " - " ASN C 332 " " NAG C 623 " - " ASN C 355 " " NAG C 627 " - " ASN C 386 " " NAG C 628 " - " ASN C 394 " " NAG C 629 " - " ASN C 411 " " NAG C 630 " - " ASN C 448 " " NAG D 901 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 619 " - " ASN E 188 " " NAG E 625 " - " ASN E 241 " " NAG E 629 " - " ASN E 276 " " NAG E 630 " - " ASN E 289 " " NAG E 634 " - " ASN E 301 " " NAG E 646 " - " ASN E 394 " " NAG E 653 " - " ASN E 448 " " NAG E 654 " - " ASN E 463 " " NAG F 901 " - " ASN F 611 " " NAG F 902 " - " ASN F 625 " " NAG G 1 " - " ASN A 134 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 363 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN B 611 " " NAG P 1 " - " ASN B 637 " " NAG Q 1 " - " ASN C 138 " " NAG R 1 " - " ASN C 145 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN E 134 " " NAG X 1 " - " ASN E 138 " " NAG Y 1 " - " ASN E 145 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 160 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 234 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 355 " " NAG h 1 " - " ASN E 363 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 398 " " NAG k 1 " - " ASN E 411 " " NAG l 1 " - " ASN F 637 " " NAG m 1 " - " ASN A 156 " " NAG n 1 " - " ASN L 24 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.2 seconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 38 sheets defined 21.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.773A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.844A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 530 through 536 Processing helix chain 'B' and resid 536 through 545 removed outlier: 3.862A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 553 removed outlier: 3.836A pdb=" N GLN B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.514A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.625A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 649 Processing helix chain 'B' and resid 650 through 654 removed outlier: 3.630A pdb=" N GLN B 653 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 654 " --> pdb=" O LYS B 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 650 through 654' Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.717A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.595A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.797A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 407 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.765A pdb=" N ILE D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 547 through 552 removed outlier: 3.684A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.614A pdb=" N GLU D 634 " --> pdb=" O TRP D 631 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 635 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 653 removed outlier: 4.338A pdb=" N LYS D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 4.289A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.528A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.545A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.679A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.699A pdb=" N ARG E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.842A pdb=" N ILE F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.573A pdb=" N VAL F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 546 through 552 removed outlier: 3.691A pdb=" N GLN F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 555 No H-bonds generated for 'chain 'F' and resid 553 through 555' Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 620 through 625 Processing helix chain 'F' and resid 628 through 635 removed outlier: 4.439A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 653 removed outlier: 3.638A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN F 650 " --> pdb=" O ILE F 646 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.389A pdb=" N LYS H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 121 through 126 removed outlier: 4.611A pdb=" N GLN L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.946A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.148A pdb=" N PHE H 100J" --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TYR A 173 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.609A pdb=" N LEU A 452 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 416 Processing sheet with id=AA8, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.850A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.105A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.071A pdb=" N ILE C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.613A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.836A pdb=" N ILE C 424 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 434 " --> pdb=" O ILE C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AC2, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'E' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 3.814A pdb=" N ILE E 434 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE E 424 " --> pdb=" O ILE E 434 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.661A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.652A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.240A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 120 through 130 removed outlier: 5.846A pdb=" N ALA H 137 " --> pdb=" O PRO H 126 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER H 128 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR H 135 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 120 through 130 removed outlier: 5.846A pdb=" N ALA H 137 " --> pdb=" O PRO H 126 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER H 128 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR H 135 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 169 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 150 through 154 Processing sheet with id=AD6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AD7, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AD8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.114A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.881A pdb=" N THR L 131 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU L 180 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL L 133 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU L 178 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU L 135 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER L 176 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER L 137 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA L 174 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.881A pdb=" N THR L 131 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU L 180 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL L 133 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU L 178 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU L 135 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER L 176 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER L 137 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA L 174 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 145 through 150 609 hydrogen bonds defined for protein. 1563 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: 6.20 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6266 1.36 - 1.50: 5752 1.50 - 1.64: 8172 1.64 - 1.78: 3 1.78 - 1.93: 151 Bond restraints: 20344 Sorted by residual: bond pdb=" C2 MAN G 4 " pdb=" O2 MAN G 4 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.926 -0.118 3.30e-02 9.18e+02 1.29e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.923 -0.115 3.30e-02 9.18e+02 1.22e+01 bond pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 1.808 1.919 -0.111 3.30e-02 9.18e+02 1.13e+01 ... (remaining 20339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 26210 1.95 - 3.90: 1124 3.90 - 5.85: 267 5.85 - 7.80: 45 7.80 - 9.75: 6 Bond angle restraints: 27652 Sorted by residual: angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C GLU D 560 " pdb=" N ALA D 561 " pdb=" CA ALA D 561 " ideal model delta sigma weight residual 121.81 114.19 7.62 1.83e+00 2.99e-01 1.73e+01 angle pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta sigma weight residual 125.02 132.01 -6.99 1.76e+00 3.23e-01 1.58e+01 angle pdb=" C GLU F 560 " pdb=" N ALA F 561 " pdb=" CA ALA F 561 " ideal model delta sigma weight residual 120.88 114.91 5.97 1.62e+00 3.81e-01 1.36e+01 angle pdb=" C VAL E 68 " pdb=" N TRP E 69 " pdb=" CA TRP E 69 " ideal model delta sigma weight residual 125.02 131.17 -6.15 1.76e+00 3.23e-01 1.22e+01 ... (remaining 27647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 12778 24.22 - 48.43: 850 48.43 - 72.65: 193 72.65 - 96.86: 156 96.86 - 121.08: 101 Dihedral angle restraints: 14078 sinusoidal: 7420 harmonic: 6658 Sorted by residual: dihedral pdb=" CA GLU L 198 " pdb=" C GLU L 198 " pdb=" N GLY L 199 " pdb=" CA GLY L 199 " ideal model delta harmonic sigma weight residual -180.00 -128.94 -51.06 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA GLY E 187 " pdb=" C GLY E 187 " pdb=" N ASN E 188 " pdb=" CA ASN E 188 " ideal model delta harmonic sigma weight residual 180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 176.09 -83.09 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 14075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3407 0.140 - 0.280: 108 0.280 - 0.420: 19 0.420 - 0.560: 3 0.560 - 0.700: 1 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.14e+02 chirality pdb=" C1 MAN a 4 " pdb=" O6 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3535 not shown) Planarity restraints: 3417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 409 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO E 410 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 410 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 410 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 114 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" CD GLN C 114 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN C 114 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN C 114 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 201 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO H 202 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " 0.033 5.00e-02 4.00e+02 ... (remaining 3414 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 512 2.65 - 3.21: 19815 3.21 - 3.77: 30347 3.77 - 4.34: 41040 4.34 - 4.90: 65395 Nonbonded interactions: 157109 Sorted by model distance: nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.086 3.040 nonbonded pdb=" OG SER A 132 " pdb=" OD1 ASN A 156 " model vdw 2.086 3.040 nonbonded pdb=" O ILE F 635 " pdb=" OG1 THR F 639 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR L 18 " pdb=" O ILE L 75 " model vdw 2.088 3.040 nonbonded pdb=" O ILE B 635 " pdb=" OG1 THR B 639 " model vdw 2.090 3.040 ... (remaining 157104 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 32 through 507 or resid 601 through 628)) selection = (chain 'C' and (resid 32 through 507 or resid 601 through 622)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 521 through 664 or resid 901)) } ncs_group { reference = (chain 'G' and (resid 1 or resid 4)) selection = (chain 'a' and (resid 2 or resid 5)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'h' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.990 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 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 : 0.008 0.254 20535 Z= 0.393 Angle : 1.255 25.283 28170 Z= 0.569 Chirality : 0.068 0.700 3538 Planarity : 0.004 0.067 3341 Dihedral : 21.250 121.075 9650 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.29 % Allowed : 2.26 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.46 (0.14), residues: 2285 helix: -2.64 (0.20), residues: 370 sheet: -2.93 (0.18), residues: 517 loop : -3.21 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.012 0.001 HIS E 105 PHE 0.013 0.001 PHE L 49 TYR 0.012 0.001 TYR B 643 ARG 0.003 0.000 ARG C 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 76) link_NAG-ASN : angle 3.48308 ( 228) link_ALPHA1-6 : bond 0.00435 ( 5) link_ALPHA1-6 : angle 2.35026 ( 15) link_BETA1-2 : bond 0.00892 ( 1) link_BETA1-2 : angle 5.80544 ( 3) link_BETA1-4 : bond 0.00795 ( 54) link_BETA1-4 : angle 4.26103 ( 162) link_ALPHA1-3 : bond 0.00630 ( 4) link_ALPHA1-3 : angle 3.05747 ( 12) hydrogen bonds : bond 0.13504 ( 583) hydrogen bonds : angle 7.28839 ( 1563) link_BETA1-6 : bond 0.00218 ( 2) link_BETA1-6 : angle 1.88876 ( 6) SS BOND : bond 0.11507 ( 46) SS BOND : angle 12.31820 ( 92) covalent geometry : bond 0.00605 (20344) covalent geometry : angle 0.93893 (27652) Misc. bond : bond 0.00287 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 284 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8828 (mt) cc_final: 0.8352 (tp) REVERT: A 382 PHE cc_start: 0.8448 (m-80) cc_final: 0.8050 (m-80) REVERT: A 504 ARG cc_start: 0.3644 (ttm-80) cc_final: 0.2816 (ptm160) REVERT: B 589 ASP cc_start: 0.8422 (t0) cc_final: 0.8172 (t0) REVERT: C 382 PHE cc_start: 0.7057 (m-80) cc_final: 0.6596 (m-80) REVERT: D 541 VAL cc_start: 0.7128 (t) cc_final: 0.6854 (m) REVERT: D 645 LEU cc_start: 0.9283 (mt) cc_final: 0.9075 (pp) REVERT: E 352 TYR cc_start: 0.4459 (p90) cc_final: 0.3987 (p90) REVERT: E 382 PHE cc_start: 0.7498 (m-80) cc_final: 0.6829 (m-80) REVERT: H 34 MET cc_start: 0.6868 (mmm) cc_final: 0.6410 (mmp) outliers start: 6 outliers final: 4 residues processed: 289 average time/residue: 0.3470 time to fit residues: 149.8010 Evaluate side-chains 158 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 249 HIS ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN C 440 GLN C 461 ASN E 82 GLN E 186 ASN E 287 GLN E 344 GLN E 478 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.077457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.065217 restraints weight = 144164.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.066590 restraints weight = 98161.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.067562 restraints weight = 73803.732| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.250 20535 Z= 0.403 Angle : 1.345 24.412 28170 Z= 0.605 Chirality : 0.065 0.621 3538 Planarity : 0.006 0.053 3341 Dihedral : 17.100 109.862 5378 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.51 % Favored : 88.32 % Rotamer: Outliers : 0.59 % Allowed : 9.38 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % 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: -3.96 (0.15), residues: 2285 helix: -2.06 (0.22), residues: 375 sheet: -2.36 (0.21), residues: 480 loop : -3.04 (0.14), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 395 HIS 0.021 0.003 HIS A 105 PHE 0.026 0.003 PHE A 210 TYR 0.020 0.003 TYR A 352 ARG 0.008 0.001 ARG E 216 Details of bonding type rmsd link_NAG-ASN : bond 0.01021 ( 76) link_NAG-ASN : angle 4.67032 ( 228) link_ALPHA1-6 : bond 0.00686 ( 5) link_ALPHA1-6 : angle 2.54187 ( 15) link_BETA1-2 : bond 0.01261 ( 1) link_BETA1-2 : angle 5.89336 ( 3) link_BETA1-4 : bond 0.01002 ( 54) link_BETA1-4 : angle 3.83452 ( 162) link_ALPHA1-3 : bond 0.01325 ( 4) link_ALPHA1-3 : angle 3.84976 ( 12) hydrogen bonds : bond 0.05331 ( 583) hydrogen bonds : angle 7.16326 ( 1563) link_BETA1-6 : bond 0.00618 ( 2) link_BETA1-6 : angle 3.15018 ( 6) SS BOND : bond 0.11569 ( 46) SS BOND : angle 12.27277 ( 92) covalent geometry : bond 0.00652 (20344) covalent geometry : angle 1.03009 (27652) Misc. bond : bond 0.00238 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8573 (ptt) cc_final: 0.8359 (ptt) REVERT: A 382 PHE cc_start: 0.8024 (m-80) cc_final: 0.7748 (m-80) REVERT: A 504 ARG cc_start: 0.3570 (ttm-80) cc_final: 0.2601 (ptm160) REVERT: B 589 ASP cc_start: 0.8559 (t0) cc_final: 0.8315 (t0) REVERT: B 632 ASP cc_start: 0.7650 (m-30) cc_final: 0.7322 (m-30) REVERT: C 242 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8189 (p) REVERT: C 382 PHE cc_start: 0.7093 (m-10) cc_final: 0.6714 (m-80) REVERT: D 541 VAL cc_start: 0.7295 (t) cc_final: 0.7072 (m) REVERT: E 72 HIS cc_start: 0.7062 (m90) cc_final: 0.6809 (p-80) REVERT: E 104 MET cc_start: 0.8889 (ttp) cc_final: 0.8044 (tmm) REVERT: E 271 MET cc_start: 0.7526 (ttm) cc_final: 0.7173 (ttm) REVERT: E 330 HIS cc_start: 0.7674 (m-70) cc_final: 0.7395 (m90) REVERT: E 373 THR cc_start: 0.7962 (t) cc_final: 0.7659 (m) REVERT: E 475 MET cc_start: 0.8022 (pmm) cc_final: 0.6984 (pmm) REVERT: H 55 MET cc_start: 0.8151 (mtp) cc_final: 0.7891 (mtm) outliers start: 12 outliers final: 2 residues processed: 195 average time/residue: 0.3441 time to fit residues: 100.2810 Evaluate side-chains 125 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN E 343 HIS ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95AHIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.065051 restraints weight = 142553.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.066399 restraints weight = 96700.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.067365 restraints weight = 72767.777| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.263 20535 Z= 0.361 Angle : 1.241 26.877 28170 Z= 0.560 Chirality : 0.061 0.550 3538 Planarity : 0.005 0.054 3341 Dihedral : 14.259 110.940 5378 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.65 (0.15), residues: 2285 helix: -1.78 (0.23), residues: 373 sheet: -2.00 (0.22), residues: 435 loop : -2.90 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 395 HIS 0.017 0.002 HIS A 105 PHE 0.025 0.002 PHE E 382 TYR 0.038 0.002 TYR F 643 ARG 0.006 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 76) link_NAG-ASN : angle 4.05323 ( 228) link_ALPHA1-6 : bond 0.00836 ( 5) link_ALPHA1-6 : angle 2.01450 ( 15) link_BETA1-2 : bond 0.00921 ( 1) link_BETA1-2 : angle 5.35421 ( 3) link_BETA1-4 : bond 0.00948 ( 54) link_BETA1-4 : angle 3.49331 ( 162) link_ALPHA1-3 : bond 0.01756 ( 4) link_ALPHA1-3 : angle 2.85722 ( 12) hydrogen bonds : bond 0.04841 ( 583) hydrogen bonds : angle 7.20654 ( 1563) link_BETA1-6 : bond 0.00191 ( 2) link_BETA1-6 : angle 2.21706 ( 6) SS BOND : bond 0.11751 ( 46) SS BOND : angle 12.13768 ( 92) covalent geometry : bond 0.00510 (20344) covalent geometry : angle 0.92883 (27652) Misc. bond : bond 0.00258 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.5221 (t60) cc_final: 0.4687 (t60) REVERT: A 271 MET cc_start: 0.8162 (tpp) cc_final: 0.7794 (tpp) REVERT: B 589 ASP cc_start: 0.8860 (t0) cc_final: 0.8624 (t0) REVERT: B 643 TYR cc_start: 0.8498 (m-80) cc_final: 0.8256 (m-80) REVERT: C 150 MET cc_start: 0.5059 (ptt) cc_final: 0.4459 (pmm) REVERT: C 308 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7850 (tpp80) REVERT: C 382 PHE cc_start: 0.7422 (m-10) cc_final: 0.6903 (m-80) REVERT: C 395 TRP cc_start: 0.5970 (OUTLIER) cc_final: 0.5644 (m-10) REVERT: D 541 VAL cc_start: 0.7249 (t) cc_final: 0.6998 (m) REVERT: D 588 ARG cc_start: 0.8351 (tpt90) cc_final: 0.7961 (tpp-160) REVERT: D 639 THR cc_start: 0.8489 (p) cc_final: 0.8232 (p) REVERT: E 72 HIS cc_start: 0.6950 (m90) cc_final: 0.6720 (p-80) REVERT: E 271 MET cc_start: 0.7555 (ttm) cc_final: 0.7046 (ttm) REVERT: E 373 THR cc_start: 0.7839 (t) cc_final: 0.7601 (m) REVERT: E 475 MET cc_start: 0.7795 (pmm) cc_final: 0.7015 (pmm) REVERT: H 55 MET cc_start: 0.7995 (mtp) cc_final: 0.7732 (mtm) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.3573 time to fit residues: 92.8319 Evaluate side-chains 120 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 157 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 203 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 105 optimal weight: 0.5980 chunk 137 optimal weight: 0.0870 chunk 215 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN F 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.080014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.067638 restraints weight = 142603.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.069060 restraints weight = 95899.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.070045 restraints weight = 71756.847| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.263 20535 Z= 0.324 Angle : 1.163 26.190 28170 Z= 0.522 Chirality : 0.058 0.556 3538 Planarity : 0.004 0.049 3341 Dihedral : 11.787 109.248 5378 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.26 (0.16), residues: 2285 helix: -1.23 (0.25), residues: 377 sheet: -1.70 (0.22), residues: 464 loop : -2.73 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 571 HIS 0.017 0.002 HIS A 105 PHE 0.023 0.001 PHE E 382 TYR 0.021 0.002 TYR E 352 ARG 0.007 0.001 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 76) link_NAG-ASN : angle 3.85915 ( 228) link_ALPHA1-6 : bond 0.00740 ( 5) link_ALPHA1-6 : angle 1.85455 ( 15) link_BETA1-2 : bond 0.01038 ( 1) link_BETA1-2 : angle 5.10186 ( 3) link_BETA1-4 : bond 0.00852 ( 54) link_BETA1-4 : angle 3.29213 ( 162) link_ALPHA1-3 : bond 0.01567 ( 4) link_ALPHA1-3 : angle 2.51084 ( 12) hydrogen bonds : bond 0.04099 ( 583) hydrogen bonds : angle 6.74723 ( 1563) link_BETA1-6 : bond 0.00236 ( 2) link_BETA1-6 : angle 2.10376 ( 6) SS BOND : bond 0.11936 ( 46) SS BOND : angle 12.06286 ( 92) covalent geometry : bond 0.00340 (20344) covalent geometry : angle 0.83677 (27652) Misc. bond : bond 0.00174 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.0633 (p0) cc_final: 0.0412 (p0) REVERT: A 271 MET cc_start: 0.8208 (tpp) cc_final: 0.7962 (tpp) REVERT: A 382 PHE cc_start: 0.7890 (m-80) cc_final: 0.7385 (m-10) REVERT: A 424 ILE cc_start: 0.8326 (tt) cc_final: 0.7990 (tt) REVERT: B 589 ASP cc_start: 0.8923 (t0) cc_final: 0.8623 (t0) REVERT: B 626 MET cc_start: 0.5406 (mtp) cc_final: 0.5074 (mmm) REVERT: B 632 ASP cc_start: 0.7916 (m-30) cc_final: 0.7649 (m-30) REVERT: C 150 MET cc_start: 0.5012 (ptt) cc_final: 0.4640 (pmm) REVERT: C 382 PHE cc_start: 0.7446 (m-10) cc_final: 0.6988 (m-80) REVERT: D 541 VAL cc_start: 0.7203 (t) cc_final: 0.6944 (m) REVERT: D 626 MET cc_start: 0.3932 (ttp) cc_final: 0.3596 (ttp) REVERT: E 161 MET cc_start: 0.7138 (tpt) cc_final: 0.6895 (tpt) REVERT: E 271 MET cc_start: 0.7472 (ttm) cc_final: 0.7051 (ttm) REVERT: E 475 MET cc_start: 0.7694 (pmm) cc_final: 0.6620 (pmm) REVERT: F 544 LEU cc_start: 0.7823 (mt) cc_final: 0.7371 (tt) REVERT: F 620 ARG cc_start: 0.7319 (mmp-170) cc_final: 0.6785 (mmp-170) REVERT: H 55 MET cc_start: 0.7947 (mtp) cc_final: 0.7589 (mtm) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.3340 time to fit residues: 94.6944 Evaluate side-chains 118 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 chunk 226 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 72 HIS ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.067678 restraints weight = 142954.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.069679 restraints weight = 99419.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.070790 restraints weight = 66633.156| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.273 20535 Z= 0.319 Angle : 1.128 24.160 28170 Z= 0.510 Chirality : 0.056 0.501 3538 Planarity : 0.004 0.046 3341 Dihedral : 10.494 107.718 5378 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.06 (0.16), residues: 2285 helix: -1.10 (0.24), residues: 381 sheet: -1.61 (0.22), residues: 479 loop : -2.57 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 112 HIS 0.018 0.001 HIS A 105 PHE 0.015 0.001 PHE E 382 TYR 0.018 0.001 TYR H 100Q ARG 0.006 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 76) link_NAG-ASN : angle 3.64827 ( 228) link_ALPHA1-6 : bond 0.00781 ( 5) link_ALPHA1-6 : angle 1.77638 ( 15) link_BETA1-2 : bond 0.00960 ( 1) link_BETA1-2 : angle 4.77012 ( 3) link_BETA1-4 : bond 0.00870 ( 54) link_BETA1-4 : angle 3.11083 ( 162) link_ALPHA1-3 : bond 0.01487 ( 4) link_ALPHA1-3 : angle 2.55929 ( 12) hydrogen bonds : bond 0.03994 ( 583) hydrogen bonds : angle 6.59573 ( 1563) link_BETA1-6 : bond 0.00310 ( 2) link_BETA1-6 : angle 2.05583 ( 6) SS BOND : bond 0.11955 ( 46) SS BOND : angle 12.04013 ( 92) covalent geometry : bond 0.00325 (20344) covalent geometry : angle 0.79988 (27652) Misc. bond : bond 0.00128 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8912 (ptm) cc_final: 0.8687 (ptm) REVERT: A 271 MET cc_start: 0.8473 (tpp) cc_final: 0.7262 (mmt) REVERT: B 589 ASP cc_start: 0.9022 (t0) cc_final: 0.8765 (t0) REVERT: B 626 MET cc_start: 0.5373 (mtp) cc_final: 0.5105 (mmm) REVERT: B 632 ASP cc_start: 0.7957 (m-30) cc_final: 0.7640 (m-30) REVERT: C 150 MET cc_start: 0.4785 (ptt) cc_final: 0.4353 (pmm) REVERT: C 382 PHE cc_start: 0.7307 (m-10) cc_final: 0.6940 (m-80) REVERT: C 475 MET cc_start: 0.7899 (tmm) cc_final: 0.7539 (ppp) REVERT: D 530 MET cc_start: 0.7045 (mmp) cc_final: 0.6623 (mmm) REVERT: D 541 VAL cc_start: 0.7303 (t) cc_final: 0.7045 (m) REVERT: D 626 MET cc_start: 0.4288 (ttp) cc_final: 0.4022 (ttp) REVERT: E 271 MET cc_start: 0.7498 (ttm) cc_final: 0.6709 (ttm) REVERT: E 382 PHE cc_start: 0.7630 (m-10) cc_final: 0.7265 (m-10) REVERT: E 475 MET cc_start: 0.7708 (pmm) cc_final: 0.6641 (pmm) REVERT: F 544 LEU cc_start: 0.7942 (mt) cc_final: 0.7479 (tt) REVERT: F 601 LYS cc_start: 0.6770 (pttm) cc_final: 0.6460 (tttt) REVERT: F 620 ARG cc_start: 0.7324 (mmp-170) cc_final: 0.6875 (mmp-170) REVERT: F 632 ASP cc_start: 0.7362 (m-30) cc_final: 0.6901 (p0) REVERT: H 37 VAL cc_start: 0.8687 (t) cc_final: 0.8470 (p) REVERT: H 55 MET cc_start: 0.8072 (mtp) cc_final: 0.7691 (mtm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3501 time to fit residues: 92.8884 Evaluate side-chains 121 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.075808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.063560 restraints weight = 145580.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.064914 restraints weight = 98841.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.065827 restraints weight = 74478.916| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.253 20535 Z= 0.380 Angle : 1.247 26.160 28170 Z= 0.568 Chirality : 0.059 0.530 3538 Planarity : 0.005 0.050 3341 Dihedral : 11.007 107.420 5378 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % 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: -3.21 (0.16), residues: 2285 helix: -1.60 (0.23), residues: 368 sheet: -1.50 (0.22), residues: 469 loop : -2.63 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 395 HIS 0.022 0.002 HIS A 105 PHE 0.022 0.003 PHE A 210 TYR 0.017 0.002 TYR A 352 ARG 0.008 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00848 ( 76) link_NAG-ASN : angle 3.94592 ( 228) link_ALPHA1-6 : bond 0.00579 ( 5) link_ALPHA1-6 : angle 1.77745 ( 15) link_BETA1-2 : bond 0.00814 ( 1) link_BETA1-2 : angle 5.20097 ( 3) link_BETA1-4 : bond 0.00945 ( 54) link_BETA1-4 : angle 3.15771 ( 162) link_ALPHA1-3 : bond 0.01532 ( 4) link_ALPHA1-3 : angle 2.93077 ( 12) hydrogen bonds : bond 0.04828 ( 583) hydrogen bonds : angle 7.16347 ( 1563) link_BETA1-6 : bond 0.00049 ( 2) link_BETA1-6 : angle 2.36570 ( 6) SS BOND : bond 0.11696 ( 46) SS BOND : angle 12.14097 ( 92) covalent geometry : bond 0.00580 (20344) covalent geometry : angle 0.94670 (27652) Misc. bond : bond 0.00195 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8478 (tpp) cc_final: 0.7100 (mmm) REVERT: A 435 TYR cc_start: 0.8601 (t80) cc_final: 0.7883 (t80) REVERT: B 589 ASP cc_start: 0.9025 (t0) cc_final: 0.8753 (t0) REVERT: B 590 GLN cc_start: 0.6245 (mp10) cc_final: 0.6018 (tp40) REVERT: C 382 PHE cc_start: 0.7342 (m-10) cc_final: 0.6852 (m-80) REVERT: C 475 MET cc_start: 0.8568 (tmm) cc_final: 0.8345 (tmm) REVERT: D 541 VAL cc_start: 0.7258 (t) cc_final: 0.7011 (m) REVERT: D 626 MET cc_start: 0.4637 (ttp) cc_final: 0.4001 (ttp) REVERT: E 271 MET cc_start: 0.7543 (ttm) cc_final: 0.7003 (ttm) REVERT: E 382 PHE cc_start: 0.8045 (m-10) cc_final: 0.7665 (m-10) REVERT: E 475 MET cc_start: 0.7982 (pmm) cc_final: 0.7649 (pmm) REVERT: F 586 TYR cc_start: 0.8420 (t80) cc_final: 0.8166 (t80) REVERT: F 601 LYS cc_start: 0.6978 (pttm) cc_final: 0.6702 (tttt) REVERT: H 37 VAL cc_start: 0.8728 (t) cc_final: 0.8511 (p) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3162 time to fit residues: 78.7425 Evaluate side-chains 124 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 185 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 50 optimal weight: 0.0270 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188AASN B 652 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** 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 = 0.3928 r_free = 0.3928 target = 0.078827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.066538 restraints weight = 142158.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.067969 restraints weight = 95398.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.068962 restraints weight = 71198.072| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.264 20535 Z= 0.331 Angle : 1.156 24.231 28170 Z= 0.524 Chirality : 0.056 0.487 3538 Planarity : 0.005 0.065 3341 Dihedral : 10.161 106.277 5378 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.92 (0.16), residues: 2285 helix: -1.10 (0.25), residues: 368 sheet: -1.44 (0.22), residues: 503 loop : -2.47 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 112 HIS 0.017 0.001 HIS A 105 PHE 0.012 0.001 PHE A 382 TYR 0.047 0.002 TYR B 643 ARG 0.008 0.001 ARG E 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 76) link_NAG-ASN : angle 3.67504 ( 228) link_ALPHA1-6 : bond 0.00698 ( 5) link_ALPHA1-6 : angle 1.59200 ( 15) link_BETA1-2 : bond 0.00922 ( 1) link_BETA1-2 : angle 4.87306 ( 3) link_BETA1-4 : bond 0.00883 ( 54) link_BETA1-4 : angle 2.99365 ( 162) link_ALPHA1-3 : bond 0.01630 ( 4) link_ALPHA1-3 : angle 2.62737 ( 12) hydrogen bonds : bond 0.04032 ( 583) hydrogen bonds : angle 6.76202 ( 1563) link_BETA1-6 : bond 0.00175 ( 2) link_BETA1-6 : angle 2.10757 ( 6) SS BOND : bond 0.12261 ( 46) SS BOND : angle 11.97501 ( 92) covalent geometry : bond 0.00353 (20344) covalent geometry : angle 0.84365 (27652) Misc. bond : bond 0.00099 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7700 (tmm) cc_final: 0.7424 (tmm) REVERT: A 271 MET cc_start: 0.8471 (tpp) cc_final: 0.7146 (mmm) REVERT: A 435 TYR cc_start: 0.8609 (t80) cc_final: 0.7867 (t80) REVERT: B 626 MET cc_start: 0.4820 (mtp) cc_final: 0.4436 (mmm) REVERT: B 643 TYR cc_start: 0.8476 (m-80) cc_final: 0.8167 (m-80) REVERT: C 382 PHE cc_start: 0.7219 (m-10) cc_final: 0.6732 (m-80) REVERT: C 408 MET cc_start: 0.5818 (mtt) cc_final: 0.4943 (mpp) REVERT: D 530 MET cc_start: 0.7159 (mmp) cc_final: 0.6941 (mmm) REVERT: D 541 VAL cc_start: 0.7380 (t) cc_final: 0.7115 (m) REVERT: D 626 MET cc_start: 0.4248 (ttp) cc_final: 0.3798 (ttp) REVERT: E 161 MET cc_start: 0.7255 (tpt) cc_final: 0.7020 (tpt) REVERT: E 271 MET cc_start: 0.7513 (ttm) cc_final: 0.6667 (ttm) REVERT: E 382 PHE cc_start: 0.7833 (m-10) cc_final: 0.7211 (m-10) REVERT: E 475 MET cc_start: 0.7805 (pmm) cc_final: 0.7039 (pmm) REVERT: F 530 MET cc_start: 0.8770 (mmp) cc_final: 0.8493 (mmm) REVERT: F 544 LEU cc_start: 0.7825 (mt) cc_final: 0.7342 (tt) REVERT: F 586 TYR cc_start: 0.8266 (t80) cc_final: 0.8016 (t80) REVERT: F 620 ARG cc_start: 0.7025 (mmp-170) cc_final: 0.6689 (mmp-170) REVERT: F 632 ASP cc_start: 0.7159 (m-30) cc_final: 0.6813 (p0) REVERT: H 37 VAL cc_start: 0.8295 (t) cc_final: 0.8071 (p) REVERT: H 55 MET cc_start: 0.7803 (mtp) cc_final: 0.7521 (mtt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3430 time to fit residues: 92.3910 Evaluate side-chains 126 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN B 656 ASN C 103 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 HIS ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.076386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.064198 restraints weight = 143989.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.065551 restraints weight = 97439.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.066495 restraints weight = 73329.193| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 20535 Z= 0.358 Angle : 1.193 24.152 28170 Z= 0.542 Chirality : 0.057 0.493 3538 Planarity : 0.005 0.060 3341 Dihedral : 10.349 105.981 5378 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.01 (0.16), residues: 2285 helix: -1.36 (0.24), residues: 376 sheet: -1.56 (0.22), residues: 489 loop : -2.45 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 69 HIS 0.017 0.002 HIS A 105 PHE 0.020 0.002 PHE A 210 TYR 0.035 0.002 TYR B 643 ARG 0.013 0.001 ARG C 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 76) link_NAG-ASN : angle 3.80337 ( 228) link_ALPHA1-6 : bond 0.00546 ( 5) link_ALPHA1-6 : angle 1.75265 ( 15) link_BETA1-2 : bond 0.00770 ( 1) link_BETA1-2 : angle 4.95244 ( 3) link_BETA1-4 : bond 0.00913 ( 54) link_BETA1-4 : angle 3.05983 ( 162) link_ALPHA1-3 : bond 0.01665 ( 4) link_ALPHA1-3 : angle 2.83583 ( 12) hydrogen bonds : bond 0.04377 ( 583) hydrogen bonds : angle 6.98943 ( 1563) link_BETA1-6 : bond 0.00057 ( 2) link_BETA1-6 : angle 2.34090 ( 6) SS BOND : bond 0.11944 ( 46) SS BOND : angle 12.03504 ( 92) covalent geometry : bond 0.00490 (20344) covalent geometry : angle 0.88594 (27652) Misc. bond : bond 0.00165 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7570 (tmm) cc_final: 0.7228 (tmm) REVERT: A 271 MET cc_start: 0.8566 (tpp) cc_final: 0.7213 (mmm) REVERT: A 435 TYR cc_start: 0.8548 (t80) cc_final: 0.7894 (t80) REVERT: A 504 ARG cc_start: 0.3042 (ttm-80) cc_final: 0.2387 (ptm160) REVERT: B 589 ASP cc_start: 0.9048 (t70) cc_final: 0.8811 (t0) REVERT: B 643 TYR cc_start: 0.8340 (m-80) cc_final: 0.8088 (m-80) REVERT: C 382 PHE cc_start: 0.7145 (m-10) cc_final: 0.6857 (m-80) REVERT: C 408 MET cc_start: 0.5188 (mtt) cc_final: 0.4974 (mtt) REVERT: D 530 MET cc_start: 0.7281 (mmp) cc_final: 0.6932 (mmm) REVERT: D 541 VAL cc_start: 0.7450 (t) cc_final: 0.7218 (m) REVERT: D 626 MET cc_start: 0.4604 (ttp) cc_final: 0.3776 (ttp) REVERT: D 647 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7619 (mt-10) REVERT: E 271 MET cc_start: 0.7455 (ttm) cc_final: 0.6596 (ttm) REVERT: E 382 PHE cc_start: 0.7985 (m-10) cc_final: 0.7646 (m-10) REVERT: F 544 LEU cc_start: 0.7816 (mt) cc_final: 0.7366 (tt) REVERT: F 586 TYR cc_start: 0.8375 (t80) cc_final: 0.8134 (t80) REVERT: F 601 LYS cc_start: 0.6028 (tttt) cc_final: 0.5630 (tttm) REVERT: F 620 ARG cc_start: 0.7721 (mmp-170) cc_final: 0.7413 (mmp-170) REVERT: F 632 ASP cc_start: 0.6915 (m-30) cc_final: 0.6517 (p0) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3289 time to fit residues: 78.7696 Evaluate side-chains 120 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 41 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 220 optimal weight: 30.0000 chunk 126 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 197 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** 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 = 0.3910 r_free = 0.3910 target = 0.078195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.065719 restraints weight = 141684.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.067152 restraints weight = 95119.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.068144 restraints weight = 71132.558| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.274 20535 Z= 0.331 Angle : 1.156 26.556 28170 Z= 0.523 Chirality : 0.056 0.465 3538 Planarity : 0.005 0.064 3341 Dihedral : 9.851 105.466 5378 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.91 (0.16), residues: 2285 helix: -1.17 (0.24), residues: 378 sheet: -1.62 (0.21), residues: 526 loop : -2.37 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 427 HIS 0.019 0.001 HIS E 105 PHE 0.012 0.001 PHE A 317 TYR 0.038 0.002 TYR B 643 ARG 0.005 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 76) link_NAG-ASN : angle 3.71891 ( 228) link_ALPHA1-6 : bond 0.00680 ( 5) link_ALPHA1-6 : angle 1.62434 ( 15) link_BETA1-2 : bond 0.00864 ( 1) link_BETA1-2 : angle 4.78715 ( 3) link_BETA1-4 : bond 0.00837 ( 54) link_BETA1-4 : angle 2.93103 ( 162) link_ALPHA1-3 : bond 0.01661 ( 4) link_ALPHA1-3 : angle 2.69380 ( 12) hydrogen bonds : bond 0.04001 ( 583) hydrogen bonds : angle 6.74365 ( 1563) link_BETA1-6 : bond 0.00165 ( 2) link_BETA1-6 : angle 2.22260 ( 6) SS BOND : bond 0.12238 ( 46) SS BOND : angle 11.99963 ( 92) covalent geometry : bond 0.00360 (20344) covalent geometry : angle 0.84296 (27652) Misc. bond : bond 0.00115 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7583 (tmm) cc_final: 0.7302 (tmm) REVERT: A 122 LEU cc_start: 0.9084 (mt) cc_final: 0.8870 (mt) REVERT: A 161 MET cc_start: 0.7146 (tpp) cc_final: 0.6493 (tmm) REVERT: A 271 MET cc_start: 0.8479 (tpp) cc_final: 0.7048 (mmm) REVERT: A 435 TYR cc_start: 0.8563 (t80) cc_final: 0.7826 (t80) REVERT: A 504 ARG cc_start: 0.3149 (ttm-80) cc_final: 0.2201 (ptm160) REVERT: B 589 ASP cc_start: 0.9028 (t70) cc_final: 0.8780 (t0) REVERT: B 643 TYR cc_start: 0.8482 (m-80) cc_final: 0.8113 (m-80) REVERT: C 40 TYR cc_start: 0.7825 (m-80) cc_final: 0.7618 (m-10) REVERT: C 382 PHE cc_start: 0.7337 (m-10) cc_final: 0.6988 (m-80) REVERT: C 395 TRP cc_start: 0.6013 (m-10) cc_final: 0.4729 (m100) REVERT: C 408 MET cc_start: 0.5082 (mtt) cc_final: 0.4762 (mtt) REVERT: D 541 VAL cc_start: 0.7613 (t) cc_final: 0.7353 (m) REVERT: D 588 ARG cc_start: 0.8826 (ptm-80) cc_final: 0.8547 (ptm-80) REVERT: D 626 MET cc_start: 0.4416 (ttp) cc_final: 0.3859 (ttp) REVERT: D 647 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7798 (mt-10) REVERT: E 161 MET cc_start: 0.7306 (tpt) cc_final: 0.7040 (tpt) REVERT: E 271 MET cc_start: 0.7458 (ttm) cc_final: 0.6731 (ttm) REVERT: E 382 PHE cc_start: 0.7913 (m-10) cc_final: 0.7584 (m-10) REVERT: F 544 LEU cc_start: 0.7721 (mt) cc_final: 0.7269 (tt) REVERT: F 586 TYR cc_start: 0.8422 (t80) cc_final: 0.8135 (t80) REVERT: F 620 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.7498 (mmp-170) REVERT: F 632 ASP cc_start: 0.6946 (m-30) cc_final: 0.6675 (p0) REVERT: H 55 MET cc_start: 0.8677 (mtm) cc_final: 0.8299 (mtm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3341 time to fit residues: 82.7333 Evaluate side-chains 123 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 656 ASN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.075560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.063355 restraints weight = 144990.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.064694 restraints weight = 97919.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.065622 restraints weight = 73757.714| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.270 20535 Z= 0.386 Angle : 1.223 25.887 28170 Z= 0.559 Chirality : 0.058 0.478 3538 Planarity : 0.005 0.055 3341 Dihedral : 10.375 105.854 5378 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.05 (0.16), residues: 2285 helix: -1.47 (0.23), residues: 378 sheet: -1.58 (0.21), residues: 512 loop : -2.46 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP B 628 HIS 0.019 0.002 HIS E 105 PHE 0.019 0.002 PHE A 383 TYR 0.031 0.002 TYR B 643 ARG 0.034 0.001 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 76) link_NAG-ASN : angle 3.86393 ( 228) link_ALPHA1-6 : bond 0.00507 ( 5) link_ALPHA1-6 : angle 1.80466 ( 15) link_BETA1-2 : bond 0.00702 ( 1) link_BETA1-2 : angle 4.98220 ( 3) link_BETA1-4 : bond 0.00923 ( 54) link_BETA1-4 : angle 3.02020 ( 162) link_ALPHA1-3 : bond 0.01709 ( 4) link_ALPHA1-3 : angle 2.84464 ( 12) hydrogen bonds : bond 0.04616 ( 583) hydrogen bonds : angle 7.11820 ( 1563) link_BETA1-6 : bond 0.00078 ( 2) link_BETA1-6 : angle 2.61414 ( 6) SS BOND : bond 0.12715 ( 46) SS BOND : angle 11.84520 ( 92) covalent geometry : bond 0.00536 (20344) covalent geometry : angle 0.93338 (27652) Misc. bond : bond 0.00181 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.5154 (t60) cc_final: 0.4794 (t-100) REVERT: A 104 MET cc_start: 0.7661 (tmm) cc_final: 0.7326 (tmm) REVERT: A 161 MET cc_start: 0.7556 (tpp) cc_final: 0.7048 (tmm) REVERT: A 271 MET cc_start: 0.8424 (tpp) cc_final: 0.7309 (mmm) REVERT: A 504 ARG cc_start: 0.2474 (ttm-80) cc_final: 0.1995 (ptm160) REVERT: B 589 ASP cc_start: 0.9116 (t70) cc_final: 0.8871 (t0) REVERT: B 590 GLN cc_start: 0.6071 (mp10) cc_final: 0.5781 (mp10) REVERT: B 643 TYR cc_start: 0.8383 (m-80) cc_final: 0.7872 (m-80) REVERT: C 382 PHE cc_start: 0.7186 (m-10) cc_final: 0.6971 (m-80) REVERT: C 408 MET cc_start: 0.5278 (mtt) cc_final: 0.4889 (mtt) REVERT: D 530 MET cc_start: 0.7353 (mmp) cc_final: 0.6755 (mmm) REVERT: D 541 VAL cc_start: 0.7624 (t) cc_final: 0.7383 (m) REVERT: D 588 ARG cc_start: 0.8927 (ptm-80) cc_final: 0.8681 (ptm-80) REVERT: D 626 MET cc_start: 0.4753 (ttp) cc_final: 0.3955 (ttp) REVERT: D 647 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7627 (mt-10) REVERT: E 271 MET cc_start: 0.7441 (ttm) cc_final: 0.6568 (ttm) REVERT: E 330 HIS cc_start: 0.7982 (m-70) cc_final: 0.7754 (m90) REVERT: E 382 PHE cc_start: 0.7789 (m-10) cc_final: 0.7139 (m-10) REVERT: F 544 LEU cc_start: 0.7957 (mt) cc_final: 0.7382 (tt) REVERT: F 586 TYR cc_start: 0.8614 (t80) cc_final: 0.8382 (t80) REVERT: F 632 ASP cc_start: 0.7070 (m-30) cc_final: 0.6690 (p0) REVERT: F 643 TYR cc_start: 0.8943 (m-80) cc_final: 0.8717 (m-80) REVERT: H 55 MET cc_start: 0.8777 (mtm) cc_final: 0.8419 (mtm) outliers start: 1 outliers final: 1 residues processed: 143 average time/residue: 0.3407 time to fit residues: 75.0694 Evaluate side-chains 117 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188AASN A 229 ASN A 300 ASN A 466 GLN C 82 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.073181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.061090 restraints weight = 147019.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062386 restraints weight = 98964.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063281 restraints weight = 74778.779| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.276 20535 Z= 0.430 Angle : 1.333 28.418 28170 Z= 0.610 Chirality : 0.062 0.486 3538 Planarity : 0.006 0.078 3341 Dihedral : 11.441 107.017 5378 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.10 % Allowed : 0.59 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.46 (0.16), residues: 2285 helix: -1.90 (0.23), residues: 374 sheet: -2.00 (0.21), residues: 505 loop : -2.63 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP B 628 HIS 0.021 0.002 HIS E 105 PHE 0.027 0.003 PHE A 210 TYR 0.030 0.003 TYR B 643 ARG 0.008 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.01098 ( 76) link_NAG-ASN : angle 4.24788 ( 228) link_ALPHA1-6 : bond 0.00462 ( 5) link_ALPHA1-6 : angle 1.89705 ( 15) link_BETA1-2 : bond 0.00652 ( 1) link_BETA1-2 : angle 5.57166 ( 3) link_BETA1-4 : bond 0.01002 ( 54) link_BETA1-4 : angle 3.21793 ( 162) link_ALPHA1-3 : bond 0.01964 ( 4) link_ALPHA1-3 : angle 3.08042 ( 12) hydrogen bonds : bond 0.05192 ( 583) hydrogen bonds : angle 7.72415 ( 1563) link_BETA1-6 : bond 0.00275 ( 2) link_BETA1-6 : angle 2.75715 ( 6) SS BOND : bond 0.12551 ( 46) SS BOND : angle 11.90445 ( 92) covalent geometry : bond 0.00679 (20344) covalent geometry : angle 1.05732 (27652) Misc. bond : bond 0.00189 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5748.92 seconds wall clock time: 101 minutes 47.43 seconds (6107.43 seconds total)