Starting phenix.real_space_refine on Thu Mar 5 07:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ulc_20813/03_2026/6ulc_20813_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ulc_20813/03_2026/6ulc_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_20813/03_2026/6ulc_20813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ulc_20813/03_2026/6ulc_20813.map" model { file = "/net/cci-nas-00/data/ceres_data/6ulc_20813/03_2026/6ulc_20813_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ulc_20813/03_2026/6ulc_20813_neut.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.10, per 1000 atoms: 0.26 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: 2.49 Conformation dependent library (CDL) restraints added in 951.0 milliseconds 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: 0.76 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: 3.89 Time building geometry restraints manager: 3.00 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 628) selection = (chain 'C' and resid 32 through 622) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and resid 521 through 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.520 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- 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 : 5.60 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (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 ARG 0.003 0.000 ARG C 216 TYR 0.012 0.001 TYR B 643 PHE 0.013 0.001 PHE L 49 TRP 0.012 0.001 TRP C 353 HIS 0.012 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00605 (20344) covalent geometry : angle 0.93893 (27652) SS BOND : bond 0.11507 ( 46) SS BOND : angle 12.31820 ( 92) hydrogen bonds : bond 0.13504 ( 583) hydrogen bonds : angle 7.28839 ( 1563) Misc. bond : bond 0.00287 ( 3) link_ALPHA1-3 : bond 0.00630 ( 4) link_ALPHA1-3 : angle 3.05747 ( 12) 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_BETA1-6 : bond 0.00218 ( 2) link_BETA1-6 : angle 1.88876 ( 6) link_NAG-ASN : bond 0.00790 ( 76) link_NAG-ASN : angle 3.48308 ( 228) *********************** 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 : 0.880 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: 0.8347 (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: 0.8169 (t0) REVERT: C 382 PHE cc_start: 0.7057 (m-80) cc_final: 0.6602 (m-80) REVERT: D 541 VAL cc_start: 0.7127 (t) cc_final: 0.6872 (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: 0.3990 (p90) REVERT: E 382 PHE cc_start: 0.7498 (m-80) cc_final: 0.6767 (m-80) REVERT: H 34 MET cc_start: 0.6868 (mmm) cc_final: 0.6412 (mmp) outliers start: 6 outliers final: 4 residues processed: 289 average time/residue: 0.1645 time to fit residues: 71.2500 Evaluate side-chains 159 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.2980 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 249 HIS C 328 GLN C 428 GLN C 440 GLN C 461 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 186 ASN E 344 GLN E 377 ASN E 478 ASN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.078990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.066713 restraints weight = 144132.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.068112 restraints weight = 97336.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.069058 restraints weight = 73002.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.069762 restraints weight = 59538.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.070241 restraints weight = 50995.011| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 20535 Z= 0.371 Angle : 1.289 24.049 28170 Z= 0.578 Chirality : 0.063 0.535 3538 Planarity : 0.005 0.053 3341 Dihedral : 16.970 109.875 5378 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.72 % Favored : 89.19 % Rotamer: Outliers : 0.54 % Allowed : 8.20 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.15), residues: 2285 helix: -1.90 (0.22), residues: 377 sheet: -2.35 (0.21), residues: 463 loop : -2.99 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 216 TYR 0.024 0.002 TYR D 643 PHE 0.021 0.002 PHE A 210 TRP 0.031 0.002 TRP C 395 HIS 0.021 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00547 (20344) covalent geometry : angle 0.96560 (27652) SS BOND : bond 0.11563 ( 46) SS BOND : angle 12.24489 ( 92) hydrogen bonds : bond 0.04898 ( 583) hydrogen bonds : angle 6.90045 ( 1563) Misc. bond : bond 0.00243 ( 3) link_ALPHA1-3 : bond 0.01660 ( 4) link_ALPHA1-3 : angle 3.59241 ( 12) link_ALPHA1-6 : bond 0.00712 ( 5) link_ALPHA1-6 : angle 2.47635 ( 15) link_BETA1-2 : bond 0.01197 ( 1) link_BETA1-2 : angle 5.73278 ( 3) link_BETA1-4 : bond 0.01083 ( 54) link_BETA1-4 : angle 3.71292 ( 162) link_BETA1-6 : bond 0.00384 ( 2) link_BETA1-6 : angle 2.63469 ( 6) link_NAG-ASN : bond 0.01044 ( 76) link_NAG-ASN : angle 4.51019 ( 228) *********************** 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 202 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.741 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: A 95 MET cc_start: 0.8365 (ptt) cc_final: 0.8165 (ptt) REVERT: A 163 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6426 (t) REVERT: A 382 PHE cc_start: 0.8303 (m-80) cc_final: 0.8043 (m-80) REVERT: A 504 ARG cc_start: 0.3465 (ttm-80) cc_final: 0.2578 (ptm160) REVERT: B 589 ASP cc_start: 0.8535 (t0) cc_final: 0.8277 (t0) REVERT: B 632 ASP cc_start: 0.7508 (m-30) cc_final: 0.7230 (m-30) REVERT: C 242 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 382 PHE cc_start: 0.6924 (m-10) cc_final: 0.6625 (m-80) REVERT: D 541 VAL cc_start: 0.7209 (t) cc_final: 0.6922 (m) REVERT: E 104 MET cc_start: 0.8691 (ttp) cc_final: 0.8249 (tmm) REVERT: E 271 MET cc_start: 0.7489 (ttm) cc_final: 0.7209 (ttm) REVERT: E 373 THR cc_start: 0.7684 (t) cc_final: 0.7412 (m) REVERT: E 475 MET cc_start: 0.8132 (pmm) cc_final: 0.7216 (pmm) REVERT: F 646 ILE cc_start: 0.8020 (mt) cc_final: 0.7817 (mm) REVERT: H 194 TYR cc_start: 0.5577 (m-10) cc_final: 0.4761 (m-80) REVERT: L 1 GLN cc_start: 0.5933 (tm-30) cc_final: 0.5199 (tp-100) outliers start: 11 outliers final: 2 residues processed: 199 average time/residue: 0.1635 time to fit residues: 48.9491 Evaluate side-chains 130 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 HIS H 100PASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.080164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.067838 restraints weight = 143380.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.069272 restraints weight = 96469.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.070280 restraints weight = 71942.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.070990 restraints weight = 57998.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.071469 restraints weight = 49535.696| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.256 20535 Z= 0.321 Angle : 1.182 27.730 28170 Z= 0.529 Chirality : 0.059 0.503 3538 Planarity : 0.004 0.051 3341 Dihedral : 13.857 110.390 5378 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.10 % Allowed : 4.32 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.15), residues: 2285 helix: -1.33 (0.24), residues: 377 sheet: -2.04 (0.21), residues: 492 loop : -2.80 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 96 TYR 0.044 0.002 TYR F 643 PHE 0.032 0.002 PHE E 382 TRP 0.037 0.002 TRP C 395 HIS 0.016 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00358 (20344) covalent geometry : angle 0.85167 (27652) SS BOND : bond 0.11681 ( 46) SS BOND : angle 12.16395 ( 92) hydrogen bonds : bond 0.04238 ( 583) hydrogen bonds : angle 6.69297 ( 1563) Misc. bond : bond 0.00550 ( 3) link_ALPHA1-3 : bond 0.01761 ( 4) link_ALPHA1-3 : angle 2.68760 ( 12) link_ALPHA1-6 : bond 0.00884 ( 5) link_ALPHA1-6 : angle 2.12231 ( 15) link_BETA1-2 : bond 0.00956 ( 1) link_BETA1-2 : angle 5.23088 ( 3) link_BETA1-4 : bond 0.00889 ( 54) link_BETA1-4 : angle 3.42418 ( 162) link_BETA1-6 : bond 0.00127 ( 2) link_BETA1-6 : angle 1.83391 ( 6) link_NAG-ASN : bond 0.00790 ( 76) link_NAG-ASN : angle 3.94264 ( 228) *********************** 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 186 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.971 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: A 69 TRP cc_start: 0.4977 (t60) cc_final: 0.4758 (t60) REVERT: A 271 MET cc_start: 0.8076 (tpp) cc_final: 0.7674 (tpp) REVERT: B 589 ASP cc_start: 0.8670 (t0) cc_final: 0.8372 (t0) REVERT: C 150 MET cc_start: 0.4692 (ptt) cc_final: 0.4419 (pmm) REVERT: C 382 PHE cc_start: 0.6980 (m-10) cc_final: 0.6670 (m-80) REVERT: C 475 MET cc_start: 0.8048 (tmm) cc_final: 0.7815 (tmm) REVERT: D 541 VAL cc_start: 0.7144 (t) cc_final: 0.6820 (m) REVERT: D 647 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7391 (mt-10) REVERT: E 104 MET cc_start: 0.8467 (ttp) cc_final: 0.7762 (tmm) REVERT: E 271 MET cc_start: 0.7508 (ttm) cc_final: 0.7051 (ttm) REVERT: E 475 MET cc_start: 0.7416 (pmm) cc_final: 0.7090 (pmm) REVERT: F 622 ILE cc_start: 0.8070 (pt) cc_final: 0.7786 (pt) REVERT: H 55 MET cc_start: 0.8037 (mtp) cc_final: 0.7822 (mtm) REVERT: H 194 TYR cc_start: 0.5650 (m-10) cc_final: 0.4810 (m-80) REVERT: L 1 GLN cc_start: 0.5800 (tm-30) cc_final: 0.4928 (tp-100) outliers start: 2 outliers final: 1 residues processed: 185 average time/residue: 0.1735 time to fit residues: 48.2813 Evaluate side-chains 124 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 197 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 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 478 ASN F 551 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.077240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.064894 restraints weight = 144500.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.066263 restraints weight = 97626.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.067221 restraints weight = 73425.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.067879 restraints weight = 59674.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.068359 restraints weight = 51506.952| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.260 20535 Z= 0.368 Angle : 1.218 28.240 28170 Z= 0.549 Chirality : 0.060 0.505 3538 Planarity : 0.005 0.050 3341 Dihedral : 12.395 109.793 5378 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.15), residues: 2285 helix: -1.52 (0.23), residues: 380 sheet: -1.79 (0.22), residues: 448 loop : -2.75 (0.14), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.036 0.002 TYR B 643 PHE 0.020 0.002 PHE L 62 TRP 0.042 0.002 TRP C 395 HIS 0.016 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00523 (20344) covalent geometry : angle 0.90983 (27652) SS BOND : bond 0.11993 ( 46) SS BOND : angle 12.04089 ( 92) hydrogen bonds : bond 0.04576 ( 583) hydrogen bonds : angle 6.96512 ( 1563) Misc. bond : bond 0.00215 ( 3) link_ALPHA1-3 : bond 0.01425 ( 4) link_ALPHA1-3 : angle 2.95518 ( 12) link_ALPHA1-6 : bond 0.00640 ( 5) link_ALPHA1-6 : angle 1.85053 ( 15) link_BETA1-2 : bond 0.00844 ( 1) link_BETA1-2 : angle 5.11865 ( 3) link_BETA1-4 : bond 0.00930 ( 54) link_BETA1-4 : angle 3.35423 ( 162) link_BETA1-6 : bond 0.00196 ( 2) link_BETA1-6 : angle 2.37613 ( 6) link_NAG-ASN : bond 0.00803 ( 76) link_NAG-ASN : angle 3.91289 ( 228) *********************** 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 165 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.733 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: A 271 MET cc_start: 0.8168 (tpp) cc_final: 0.7943 (tpp) REVERT: B 589 ASP cc_start: 0.9029 (t0) cc_final: 0.8717 (t0) REVERT: B 626 MET cc_start: 0.5126 (mtt) cc_final: 0.4865 (mtp) REVERT: B 632 ASP cc_start: 0.7941 (m-30) cc_final: 0.7693 (m-30) REVERT: B 643 TYR cc_start: 0.8702 (m-80) cc_final: 0.8451 (m-80) REVERT: C 150 MET cc_start: 0.4923 (ptt) cc_final: 0.4500 (pmm) REVERT: C 382 PHE cc_start: 0.7441 (m-10) cc_final: 0.6910 (m-80) REVERT: D 541 VAL cc_start: 0.7278 (t) cc_final: 0.7002 (m) REVERT: D 626 MET cc_start: 0.4318 (ttp) cc_final: 0.4093 (ttp) REVERT: E 271 MET cc_start: 0.7532 (ttm) cc_final: 0.6694 (ttm) REVERT: E 330 HIS cc_start: 0.7758 (m-70) cc_final: 0.7535 (m90) REVERT: E 475 MET cc_start: 0.6965 (pmm) cc_final: 0.6022 (pmm) REVERT: F 601 LYS cc_start: 0.6649 (pttm) cc_final: 0.6269 (tttt) REVERT: F 620 ARG cc_start: 0.7278 (mmp-170) cc_final: 0.6786 (mmp-170) REVERT: H 55 MET cc_start: 0.8103 (mtp) cc_final: 0.7854 (mtm) REVERT: L 47 MET cc_start: 0.7550 (mmm) cc_final: 0.7323 (tpp) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.1651 time to fit residues: 41.0730 Evaluate side-chains 122 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 81 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 45 optimal weight: 0.0060 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 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** B 652 GLN ** 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 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** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.075210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063054 restraints weight = 144451.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.064392 restraints weight = 97672.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.065327 restraints weight = 73523.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.065968 restraints weight = 59885.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066392 restraints weight = 51690.622| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.273 20535 Z= 0.398 Angle : 1.271 24.094 28170 Z= 0.582 Chirality : 0.060 0.521 3538 Planarity : 0.005 0.059 3341 Dihedral : 11.913 109.208 5378 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.15), residues: 2285 helix: -1.77 (0.23), residues: 370 sheet: -1.87 (0.21), residues: 470 loop : -2.84 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 419 TYR 0.032 0.003 TYR H 100O PHE 0.023 0.003 PHE L 62 TRP 0.040 0.003 TRP C 395 HIS 0.014 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00618 (20344) covalent geometry : angle 0.97053 (27652) SS BOND : bond 0.11854 ( 46) SS BOND : angle 12.10881 ( 92) hydrogen bonds : bond 0.05087 ( 583) hydrogen bonds : angle 7.49434 ( 1563) Misc. bond : bond 0.00193 ( 3) link_ALPHA1-3 : bond 0.01573 ( 4) link_ALPHA1-3 : angle 2.78497 ( 12) link_ALPHA1-6 : bond 0.00714 ( 5) link_ALPHA1-6 : angle 1.72994 ( 15) link_BETA1-2 : bond 0.00843 ( 1) link_BETA1-2 : angle 5.30445 ( 3) link_BETA1-4 : bond 0.00994 ( 54) link_BETA1-4 : angle 3.37017 ( 162) link_BETA1-6 : bond 0.00182 ( 2) link_BETA1-6 : angle 2.51450 ( 6) link_NAG-ASN : bond 0.00856 ( 76) link_NAG-ASN : angle 4.11994 ( 228) *********************** 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 159 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.751 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 112 TRP cc_start: 0.6648 (m-10) cc_final: 0.6408 (m-10) REVERT: A 271 MET cc_start: 0.8558 (tpp) cc_final: 0.8324 (tpp) REVERT: A 426 MET cc_start: 0.6162 (mpp) cc_final: 0.5646 (tpp) REVERT: A 435 TYR cc_start: 0.8664 (t80) cc_final: 0.7783 (t80) REVERT: B 589 ASP cc_start: 0.9044 (t0) cc_final: 0.8741 (t0) REVERT: B 590 GLN cc_start: 0.6296 (mp10) cc_final: 0.6003 (tp40) REVERT: B 643 TYR cc_start: 0.8491 (m-80) cc_final: 0.8089 (m-80) REVERT: C 382 PHE cc_start: 0.7499 (m-10) cc_final: 0.6896 (m-80) REVERT: D 530 MET cc_start: 0.7559 (mmp) cc_final: 0.6400 (mpp) REVERT: D 541 VAL cc_start: 0.6845 (t) cc_final: 0.6601 (m) REVERT: D 626 MET cc_start: 0.4533 (ttp) cc_final: 0.4008 (ttp) REVERT: E 271 MET cc_start: 0.7552 (ttm) cc_final: 0.6678 (ttm) REVERT: E 475 MET cc_start: 0.7697 (pmm) cc_final: 0.7080 (pmm) REVERT: F 601 LYS cc_start: 0.6778 (pttm) cc_final: 0.6385 (tttt) REVERT: F 646 ILE cc_start: 0.7301 (mm) cc_final: 0.7079 (mm) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1676 time to fit residues: 39.8297 Evaluate side-chains 114 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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** A 466 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 428 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN ** F 607 ASN ** 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 = 0.3851 r_free = 0.3851 target = 0.075621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.063467 restraints weight = 143909.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.064837 restraints weight = 97003.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.065786 restraints weight = 72849.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.066429 restraints weight = 59241.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.066867 restraints weight = 51152.891| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.271 20535 Z= 0.365 Angle : 1.217 25.102 28170 Z= 0.553 Chirality : 0.058 0.509 3538 Planarity : 0.005 0.049 3341 Dihedral : 11.346 108.410 5378 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.16), residues: 2285 helix: -1.60 (0.23), residues: 374 sheet: -1.67 (0.22), residues: 468 loop : -2.75 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.036 0.002 TYR A 352 PHE 0.017 0.002 PHE E 210 TRP 0.040 0.003 TRP B 628 HIS 0.019 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00512 (20344) covalent geometry : angle 0.90923 (27652) SS BOND : bond 0.11995 ( 46) SS BOND : angle 12.03803 ( 92) hydrogen bonds : bond 0.04711 ( 583) hydrogen bonds : angle 7.33043 ( 1563) Misc. bond : bond 0.00163 ( 3) link_ALPHA1-3 : bond 0.01668 ( 4) link_ALPHA1-3 : angle 2.74917 ( 12) link_ALPHA1-6 : bond 0.00683 ( 5) link_ALPHA1-6 : angle 1.73942 ( 15) link_BETA1-2 : bond 0.00892 ( 1) link_BETA1-2 : angle 5.24040 ( 3) link_BETA1-4 : bond 0.00935 ( 54) link_BETA1-4 : angle 3.23819 ( 162) link_BETA1-6 : bond 0.00218 ( 2) link_BETA1-6 : angle 2.59157 ( 6) link_NAG-ASN : bond 0.00761 ( 76) link_NAG-ASN : angle 3.96319 ( 228) *********************** 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 152 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.724 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 104 MET cc_start: 0.8637 (ppp) cc_final: 0.8144 (ppp) REVERT: A 112 TRP cc_start: 0.6368 (m-10) cc_final: 0.6122 (m-10) REVERT: A 271 MET cc_start: 0.8617 (tpp) cc_final: 0.8327 (tpp) REVERT: A 426 MET cc_start: 0.5819 (mpp) cc_final: 0.5546 (tpp) REVERT: A 435 TYR cc_start: 0.8742 (t80) cc_final: 0.7791 (t80) REVERT: A 504 ARG cc_start: 0.3229 (ttm-80) cc_final: 0.2661 (ptm160) REVERT: B 589 ASP cc_start: 0.9075 (t0) cc_final: 0.8819 (t0) REVERT: B 590 GLN cc_start: 0.6247 (mp10) cc_final: 0.5993 (tp40) REVERT: B 643 TYR cc_start: 0.8446 (m-80) cc_final: 0.8018 (m-80) REVERT: C 40 TYR cc_start: 0.8207 (m-80) cc_final: 0.7935 (m-10) REVERT: C 382 PHE cc_start: 0.7486 (m-10) cc_final: 0.6926 (m-80) REVERT: D 530 MET cc_start: 0.7401 (mmp) cc_final: 0.6139 (mpp) REVERT: D 541 VAL cc_start: 0.6775 (t) cc_final: 0.6508 (m) REVERT: D 588 ARG cc_start: 0.8508 (tpt90) cc_final: 0.8213 (tpp-160) REVERT: D 626 MET cc_start: 0.4436 (ttp) cc_final: 0.3778 (ttp) REVERT: E 271 MET cc_start: 0.7524 (ttm) cc_final: 0.6791 (ttm) REVERT: E 475 MET cc_start: 0.7683 (pmm) cc_final: 0.7031 (pmm) REVERT: F 544 LEU cc_start: 0.7762 (mt) cc_final: 0.7439 (tt) REVERT: F 545 LEU cc_start: 0.6472 (tp) cc_final: 0.6052 (tp) REVERT: F 601 LYS cc_start: 0.6935 (pttm) cc_final: 0.6633 (tttt) REVERT: H 55 MET cc_start: 0.8442 (mtm) cc_final: 0.8021 (mtm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1670 time to fit residues: 38.4118 Evaluate side-chains 117 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 72 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 199 optimal weight: 30.0000 chunk 147 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN E 246 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.076864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.064568 restraints weight = 142957.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.065970 restraints weight = 95606.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.066926 restraints weight = 71537.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.067587 restraints weight = 58035.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.068068 restraints weight = 49973.295| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4577 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= 0.338 Angle : 1.182 24.731 28170 Z= 0.534 Chirality : 0.057 0.498 3538 Planarity : 0.005 0.048 3341 Dihedral : 10.737 107.737 5378 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.16), residues: 2285 helix: -1.36 (0.24), residues: 373 sheet: -1.59 (0.22), residues: 478 loop : -2.61 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 620 TYR 0.030 0.002 TYR D 586 PHE 0.016 0.002 PHE E 382 TRP 0.054 0.003 TRP E 112 HIS 0.015 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00408 (20344) covalent geometry : angle 0.86816 (27652) SS BOND : bond 0.12087 ( 46) SS BOND : angle 12.01722 ( 92) hydrogen bonds : bond 0.04270 ( 583) hydrogen bonds : angle 7.12463 ( 1563) Misc. bond : bond 0.00130 ( 3) link_ALPHA1-3 : bond 0.01568 ( 4) link_ALPHA1-3 : angle 2.64931 ( 12) link_ALPHA1-6 : bond 0.00692 ( 5) link_ALPHA1-6 : angle 1.70065 ( 15) link_BETA1-2 : bond 0.00921 ( 1) link_BETA1-2 : angle 5.05994 ( 3) link_BETA1-4 : bond 0.00913 ( 54) link_BETA1-4 : angle 3.14354 ( 162) link_BETA1-6 : bond 0.00060 ( 2) link_BETA1-6 : angle 2.38315 ( 6) link_NAG-ASN : bond 0.00750 ( 76) link_NAG-ASN : angle 3.87440 ( 228) *********************** 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 154 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.648 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 104 MET cc_start: 0.8578 (ppp) cc_final: 0.8060 (ppp) REVERT: A 112 TRP cc_start: 0.6109 (m-10) cc_final: 0.5816 (m-10) REVERT: A 271 MET cc_start: 0.8586 (tpp) cc_final: 0.7075 (mmt) REVERT: A 426 MET cc_start: 0.6313 (mpp) cc_final: 0.5980 (tpp) REVERT: A 435 TYR cc_start: 0.8718 (t80) cc_final: 0.7825 (t80) REVERT: A 504 ARG cc_start: 0.3215 (ttm-80) cc_final: 0.2676 (ptm160) REVERT: B 643 TYR cc_start: 0.8407 (m-80) cc_final: 0.8016 (m-80) REVERT: C 382 PHE cc_start: 0.7480 (m-10) cc_final: 0.6926 (m-80) REVERT: C 475 MET cc_start: 0.7681 (tmm) cc_final: 0.6975 (tmm) REVERT: D 541 VAL cc_start: 0.7329 (t) cc_final: 0.7032 (m) REVERT: D 626 MET cc_start: 0.4360 (ttp) cc_final: 0.3837 (ttp) REVERT: E 271 MET cc_start: 0.7530 (ttm) cc_final: 0.6809 (ttm) REVERT: E 475 MET cc_start: 0.7691 (pmm) cc_final: 0.7042 (pmm) REVERT: F 544 LEU cc_start: 0.7648 (mt) cc_final: 0.7351 (tt) REVERT: F 646 ILE cc_start: 0.7336 (mm) cc_final: 0.7130 (mm) REVERT: H 55 MET cc_start: 0.8452 (mtm) cc_final: 0.8009 (mtm) REVERT: L 47 MET cc_start: 0.7706 (mmm) cc_final: 0.6997 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1533 time to fit residues: 35.6787 Evaluate side-chains 116 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 103 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 607 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.075519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063304 restraints weight = 144392.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.064664 restraints weight = 97749.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.065611 restraints weight = 73547.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.066284 restraints weight = 59811.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.066740 restraints weight = 51309.948| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.269 20535 Z= 0.363 Angle : 1.212 24.398 28170 Z= 0.549 Chirality : 0.058 0.496 3538 Planarity : 0.005 0.065 3341 Dihedral : 10.836 107.450 5378 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 0.10 % Allowed : 1.62 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.16), residues: 2285 helix: -1.39 (0.24), residues: 373 sheet: -1.74 (0.21), residues: 505 loop : -2.64 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.022 0.002 TYR D 586 PHE 0.014 0.002 PHE H 29 TRP 0.069 0.003 TRP B 628 HIS 0.014 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00501 (20344) covalent geometry : angle 0.90726 (27652) SS BOND : bond 0.12075 ( 46) SS BOND : angle 12.00937 ( 92) hydrogen bonds : bond 0.04512 ( 583) hydrogen bonds : angle 7.24450 ( 1563) Misc. bond : bond 0.00162 ( 3) link_ALPHA1-3 : bond 0.01269 ( 4) link_ALPHA1-3 : angle 2.61095 ( 12) link_ALPHA1-6 : bond 0.00620 ( 5) link_ALPHA1-6 : angle 1.73936 ( 15) link_BETA1-2 : bond 0.00805 ( 1) link_BETA1-2 : angle 5.12969 ( 3) link_BETA1-4 : bond 0.00945 ( 54) link_BETA1-4 : angle 3.16334 ( 162) link_BETA1-6 : bond 0.00095 ( 2) link_BETA1-6 : angle 2.57072 ( 6) link_NAG-ASN : bond 0.00775 ( 76) link_NAG-ASN : angle 3.91166 ( 228) *********************** 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 144 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.743 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: 0.8522 (ppp) cc_final: 0.7981 (ppp) REVERT: A 271 MET cc_start: 0.8584 (tpp) cc_final: 0.7149 (mmm) REVERT: A 382 PHE cc_start: 0.7014 (m-10) cc_final: 0.6785 (m-10) REVERT: A 435 TYR cc_start: 0.8734 (t80) cc_final: 0.7863 (t80) REVERT: A 504 ARG cc_start: 0.3254 (ttm-80) cc_final: 0.2722 (ptm160) REVERT: B 589 ASP cc_start: 0.9114 (t70) cc_final: 0.8899 (t0) REVERT: B 626 MET cc_start: 0.5489 (mtt) cc_final: 0.4823 (mmm) REVERT: B 643 TYR cc_start: 0.8351 (m-80) cc_final: 0.7973 (m-80) REVERT: C 382 PHE cc_start: 0.7719 (m-10) cc_final: 0.7153 (m-80) REVERT: D 530 MET cc_start: 0.7563 (mmp) cc_final: 0.7021 (mmm) REVERT: D 541 VAL cc_start: 0.7442 (t) cc_final: 0.7164 (m) REVERT: D 588 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8460 (tpp-160) REVERT: D 626 MET cc_start: 0.4543 (ttp) cc_final: 0.3967 (ttp) REVERT: E 271 MET cc_start: 0.7539 (ttm) cc_final: 0.6957 (ttm) REVERT: E 475 MET cc_start: 0.7837 (pmm) cc_final: 0.7185 (pmm) REVERT: F 544 LEU cc_start: 0.7415 (mt) cc_final: 0.6997 (tt) REVERT: F 601 LYS cc_start: 0.5919 (tttt) cc_final: 0.5539 (tttm) REVERT: H 55 MET cc_start: 0.8477 (mtm) cc_final: 0.8071 (mtm) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1718 time to fit residues: 37.3410 Evaluate side-chains 116 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 178 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 0.0070 chunk 103 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN D 591 GLN D 607 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 HIS H 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.077363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.065082 restraints weight = 141796.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.066487 restraints weight = 95208.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.067470 restraints weight = 71178.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.068149 restraints weight = 57544.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.068599 restraints weight = 49288.682| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 20535 Z= 0.328 Angle : 1.167 25.733 28170 Z= 0.528 Chirality : 0.057 0.496 3538 Planarity : 0.005 0.053 3341 Dihedral : 10.217 107.209 5378 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.16), residues: 2285 helix: -1.13 (0.25), residues: 373 sheet: -1.66 (0.21), residues: 525 loop : -2.53 (0.15), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 340 TYR 0.026 0.002 TYR B 643 PHE 0.014 0.002 PHE A 317 TRP 0.058 0.002 TRP B 628 HIS 0.013 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00361 (20344) covalent geometry : angle 0.85070 (27652) SS BOND : bond 0.12079 ( 46) SS BOND : angle 12.04088 ( 92) hydrogen bonds : bond 0.04040 ( 583) hydrogen bonds : angle 6.95489 ( 1563) Misc. bond : bond 0.00113 ( 3) link_ALPHA1-3 : bond 0.01666 ( 4) link_ALPHA1-3 : angle 2.70773 ( 12) link_ALPHA1-6 : bond 0.00676 ( 5) link_ALPHA1-6 : angle 1.64264 ( 15) link_BETA1-2 : bond 0.00875 ( 1) link_BETA1-2 : angle 4.92593 ( 3) link_BETA1-4 : bond 0.00871 ( 54) link_BETA1-4 : angle 3.02955 ( 162) link_BETA1-6 : bond 0.00211 ( 2) link_BETA1-6 : angle 2.49163 ( 6) link_NAG-ASN : bond 0.00765 ( 76) link_NAG-ASN : angle 3.78786 ( 228) *********************** 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 160 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.738 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: 0.8488 (ppp) cc_final: 0.7861 (ppp) REVERT: A 161 MET cc_start: 0.6369 (tpt) cc_final: 0.6159 (tmm) REVERT: A 271 MET cc_start: 0.8606 (tpp) cc_final: 0.7205 (mmm) REVERT: A 424 ILE cc_start: 0.8427 (tt) cc_final: 0.8159 (tt) REVERT: A 435 TYR cc_start: 0.8723 (t80) cc_final: 0.7908 (t80) REVERT: A 504 ARG cc_start: 0.3480 (ttm-80) cc_final: 0.2433 (ptm160) REVERT: B 589 ASP cc_start: 0.9062 (t70) cc_final: 0.8806 (t0) REVERT: B 626 MET cc_start: 0.4945 (mtt) cc_final: 0.4311 (mmm) REVERT: B 643 TYR cc_start: 0.8346 (m-80) cc_final: 0.7911 (m-80) REVERT: C 382 PHE cc_start: 0.7335 (m-10) cc_final: 0.7074 (m-80) REVERT: D 530 MET cc_start: 0.7281 (mmp) cc_final: 0.6971 (mmm) REVERT: D 541 VAL cc_start: 0.7597 (t) cc_final: 0.7320 (m) REVERT: D 588 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8369 (tpp-160) REVERT: D 626 MET cc_start: 0.4288 (ttp) cc_final: 0.3992 (ttp) REVERT: E 271 MET cc_start: 0.7427 (ttm) cc_final: 0.6654 (ttm) REVERT: E 475 MET cc_start: 0.7649 (pmm) cc_final: 0.7028 (pmm) REVERT: F 544 LEU cc_start: 0.7358 (mt) cc_final: 0.6970 (tt) REVERT: F 626 MET cc_start: 0.6970 (ttm) cc_final: 0.6651 (ttm) REVERT: F 632 ASP cc_start: 0.7629 (m-30) cc_final: 0.7184 (p0) REVERT: H 55 MET cc_start: 0.8379 (mtm) cc_final: 0.8019 (mtm) REVERT: L 47 MET cc_start: 0.7628 (mmm) cc_final: 0.6922 (mmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1555 time to fit residues: 37.7067 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 : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.076705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.064331 restraints weight = 142877.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.065724 restraints weight = 96152.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.066681 restraints weight = 71964.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.067345 restraints weight = 58288.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.067840 restraints weight = 50105.224| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4958 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= 0.349 Angle : 1.183 27.064 28170 Z= 0.535 Chirality : 0.058 0.489 3538 Planarity : 0.005 0.049 3341 Dihedral : 10.152 106.894 5378 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.16), residues: 2285 helix: -1.18 (0.25), residues: 373 sheet: -1.75 (0.21), residues: 527 loop : -2.47 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 340 TYR 0.024 0.002 TYR B 643 PHE 0.012 0.002 PHE H 90 TRP 0.077 0.003 TRP B 628 HIS 0.013 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00416 (20344) covalent geometry : angle 0.87697 (27652) SS BOND : bond 0.12467 ( 46) SS BOND : angle 11.95592 ( 92) hydrogen bonds : bond 0.04204 ( 583) hydrogen bonds : angle 7.03102 ( 1563) Misc. bond : bond 0.00139 ( 3) link_ALPHA1-3 : bond 0.01559 ( 4) link_ALPHA1-3 : angle 2.72233 ( 12) link_ALPHA1-6 : bond 0.00583 ( 5) link_ALPHA1-6 : angle 1.70984 ( 15) link_BETA1-2 : bond 0.00782 ( 1) link_BETA1-2 : angle 4.88119 ( 3) link_BETA1-4 : bond 0.00873 ( 54) link_BETA1-4 : angle 3.00534 ( 162) link_BETA1-6 : bond 0.00076 ( 2) link_BETA1-6 : angle 2.50370 ( 6) link_NAG-ASN : bond 0.00736 ( 76) link_NAG-ASN : angle 3.81887 ( 228) ********************** 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 152 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.755 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 104 MET cc_start: 0.8421 (ppp) cc_final: 0.7805 (ppp) REVERT: A 271 MET cc_start: 0.8525 (tpp) cc_final: 0.7289 (mmm) REVERT: A 435 TYR cc_start: 0.8760 (t80) cc_final: 0.7936 (t80) REVERT: A 504 ARG cc_start: 0.3505 (ttm-80) cc_final: 0.2609 (ptm160) REVERT: B 589 ASP cc_start: 0.9077 (t70) cc_final: 0.8824 (t0) REVERT: B 626 MET cc_start: 0.4711 (mtt) cc_final: 0.4151 (mmm) REVERT: B 643 TYR cc_start: 0.8305 (m-80) cc_final: 0.7912 (m-80) REVERT: C 271 MET cc_start: 0.7328 (tpp) cc_final: 0.7001 (mmt) REVERT: C 382 PHE cc_start: 0.7388 (m-10) cc_final: 0.7047 (m-80) REVERT: D 530 MET cc_start: 0.7349 (mmp) cc_final: 0.7078 (mmm) REVERT: D 541 VAL cc_start: 0.7651 (t) cc_final: 0.7368 (m) REVERT: D 588 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8356 (tpp-160) REVERT: D 626 MET cc_start: 0.4436 (ttp) cc_final: 0.3897 (ttp) REVERT: E 271 MET cc_start: 0.7445 (ttm) cc_final: 0.6575 (ttm) REVERT: E 475 MET cc_start: 0.7739 (pmm) cc_final: 0.7119 (pmm) REVERT: F 544 LEU cc_start: 0.7672 (mt) cc_final: 0.7185 (tt) REVERT: H 55 MET cc_start: 0.8449 (mtm) cc_final: 0.8055 (mtm) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1641 time to fit residues: 37.5484 Evaluate side-chains 114 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 198 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 128 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.078688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066267 restraints weight = 141923.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.067702 restraints weight = 94936.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.068687 restraints weight = 70673.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.069375 restraints weight = 56963.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.069863 restraints weight = 48791.437| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.275 20535 Z= 0.331 Angle : 1.145 28.738 28170 Z= 0.518 Chirality : 0.056 0.489 3538 Planarity : 0.005 0.045 3341 Dihedral : 9.472 105.821 5378 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.16), residues: 2285 helix: -0.94 (0.25), residues: 372 sheet: -1.60 (0.21), residues: 554 loop : -2.37 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 340 TYR 0.032 0.002 TYR F 643 PHE 0.015 0.001 PHE H 90 TRP 0.055 0.002 TRP B 628 HIS 0.015 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00328 (20344) covalent geometry : angle 0.83207 (27652) SS BOND : bond 0.12489 ( 46) SS BOND : angle 11.93082 ( 92) hydrogen bonds : bond 0.03944 ( 583) hydrogen bonds : angle 6.77475 ( 1563) Misc. bond : bond 0.00094 ( 3) link_ALPHA1-3 : bond 0.01675 ( 4) link_ALPHA1-3 : angle 2.66704 ( 12) link_ALPHA1-6 : bond 0.00691 ( 5) link_ALPHA1-6 : angle 1.62440 ( 15) link_BETA1-2 : bond 0.00847 ( 1) link_BETA1-2 : angle 4.64769 ( 3) link_BETA1-4 : bond 0.00876 ( 54) link_BETA1-4 : angle 2.88113 ( 162) link_BETA1-6 : bond 0.00239 ( 2) link_BETA1-6 : angle 2.41221 ( 6) link_NAG-ASN : bond 0.00743 ( 76) link_NAG-ASN : angle 3.71586 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.21 seconds wall clock time: 57 minutes 1.08 seconds (3421.08 seconds total)