Starting phenix.real_space_refine on Sat Sep 28 21:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/09_2024/6ulc_20813_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/09_2024/6ulc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/09_2024/6ulc_20813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/09_2024/6ulc_20813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/09_2024/6ulc_20813_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/09_2024/6ulc_20813_neut.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12400 2.51 5 N 3272 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19968 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "F" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "H" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1836 Classifications: {'peptide': 240} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 227} Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1593 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.28, per 1000 atoms: 0.61 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: 7.42 Conformation dependent library (CDL) restraints added in 2.6 seconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 38 sheets defined 21.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.773A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.844A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 530 through 536 Processing helix chain 'B' and resid 536 through 545 removed outlier: 3.862A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 553 removed outlier: 3.836A pdb=" N GLN B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.514A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.625A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 649 Processing helix chain 'B' and resid 650 through 654 removed outlier: 3.630A pdb=" N GLN B 653 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 654 " --> pdb=" O LYS B 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 650 through 654' Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.717A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.595A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.797A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 407 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.765A pdb=" N ILE D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 547 through 552 removed outlier: 3.684A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.614A pdb=" N GLU D 634 " --> pdb=" O TRP D 631 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 635 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 653 removed outlier: 4.338A pdb=" N LYS D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 4.289A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.528A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.545A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.679A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.699A pdb=" N ARG E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.842A pdb=" N ILE F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.573A pdb=" N VAL F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 546 through 552 removed outlier: 3.691A pdb=" N GLN F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 555 No H-bonds generated for 'chain 'F' and resid 553 through 555' Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 620 through 625 Processing helix chain 'F' and resid 628 through 635 removed outlier: 4.439A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 653 removed outlier: 3.638A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN F 650 " --> pdb=" O ILE F 646 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.389A pdb=" N LYS H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 121 through 126 removed outlier: 4.611A pdb=" N GLN L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.946A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.148A pdb=" N PHE H 100J" --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TYR A 173 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.609A pdb=" N LEU A 452 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 416 Processing sheet with id=AA8, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.850A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.105A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.071A pdb=" N ILE C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.613A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.836A pdb=" N ILE C 424 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 434 " --> pdb=" O ILE C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AC2, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'E' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 3.814A pdb=" N ILE E 434 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE E 424 " --> pdb=" O ILE E 434 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.661A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.652A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.240A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 120 through 130 removed outlier: 5.846A pdb=" N ALA H 137 " --> pdb=" O PRO H 126 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER H 128 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR H 135 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 120 through 130 removed outlier: 5.846A pdb=" N ALA H 137 " --> pdb=" O PRO H 126 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER H 128 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR H 135 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 169 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 150 through 154 Processing sheet with id=AD6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AD7, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AD8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.114A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.881A pdb=" N THR L 131 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU L 180 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL L 133 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU L 178 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU L 135 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER L 176 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER L 137 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA L 174 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.881A pdb=" N THR L 131 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU L 180 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL L 133 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU L 178 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU L 135 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER L 176 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER L 137 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA L 174 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 145 through 150 609 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6266 1.36 - 1.50: 5752 1.50 - 1.64: 8172 1.64 - 1.78: 3 1.78 - 1.93: 151 Bond restraints: 20344 Sorted by residual: bond pdb=" C2 MAN G 4 " pdb=" O2 MAN G 4 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.926 -0.118 3.30e-02 9.18e+02 1.29e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.923 -0.115 3.30e-02 9.18e+02 1.22e+01 bond pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 1.808 1.919 -0.111 3.30e-02 9.18e+02 1.13e+01 ... (remaining 20339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 26210 1.95 - 3.90: 1124 3.90 - 5.85: 267 5.85 - 7.80: 45 7.80 - 9.75: 6 Bond angle restraints: 27652 Sorted by residual: angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C GLU D 560 " pdb=" N ALA D 561 " pdb=" CA ALA D 561 " ideal model delta sigma weight residual 121.81 114.19 7.62 1.83e+00 2.99e-01 1.73e+01 angle pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta sigma weight residual 125.02 132.01 -6.99 1.76e+00 3.23e-01 1.58e+01 angle pdb=" C GLU F 560 " pdb=" N ALA F 561 " pdb=" CA ALA F 561 " ideal model delta sigma weight residual 120.88 114.91 5.97 1.62e+00 3.81e-01 1.36e+01 angle pdb=" C VAL E 68 " pdb=" N TRP E 69 " pdb=" CA TRP E 69 " ideal model delta sigma weight residual 125.02 131.17 -6.15 1.76e+00 3.23e-01 1.22e+01 ... (remaining 27647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 12778 24.22 - 48.43: 850 48.43 - 72.65: 193 72.65 - 96.86: 156 96.86 - 121.08: 101 Dihedral angle restraints: 14078 sinusoidal: 7420 harmonic: 6658 Sorted by residual: dihedral pdb=" CA GLU L 198 " pdb=" C GLU L 198 " pdb=" N GLY L 199 " pdb=" CA GLY L 199 " ideal model delta harmonic sigma weight residual -180.00 -128.94 -51.06 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA GLY E 187 " pdb=" C GLY E 187 " pdb=" N ASN E 188 " pdb=" CA ASN E 188 " ideal model delta harmonic sigma weight residual 180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 176.09 -83.09 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 14075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3407 0.140 - 0.280: 108 0.280 - 0.420: 19 0.420 - 0.560: 3 0.560 - 0.700: 1 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.14e+02 chirality pdb=" C1 MAN a 4 " pdb=" O6 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3535 not shown) Planarity restraints: 3417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 409 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO E 410 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 410 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 410 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 114 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" CD GLN C 114 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN C 114 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN C 114 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 201 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO H 202 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " 0.033 5.00e-02 4.00e+02 ... (remaining 3414 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 512 2.65 - 3.21: 19815 3.21 - 3.77: 30347 3.77 - 4.34: 41040 4.34 - 4.90: 65395 Nonbonded interactions: 157109 Sorted by model distance: nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.086 3.040 nonbonded pdb=" OG SER A 132 " pdb=" OD1 ASN A 156 " model vdw 2.086 3.040 nonbonded pdb=" O ILE F 635 " pdb=" OG1 THR F 639 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR L 18 " pdb=" O ILE L 75 " model vdw 2.088 3.040 nonbonded pdb=" O ILE B 635 " pdb=" OG1 THR B 639 " model vdw 2.090 3.040 ... (remaining 157104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 507 or resid 601 through 628)) selection = (chain 'C' and (resid 32 through 507 or resid 601 through 622)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 521 through 664 or resid 901)) } ncs_group { reference = (chain 'G' and (resid 1 or resid 4)) selection = (chain 'a' and (resid 2 or resid 5)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'h' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.600 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.840 ------------------------------------------------------------------------------- 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 : 0.006 0.118 20344 Z= 0.374 Angle : 0.939 9.746 27652 Z= 0.437 Chirality : 0.068 0.700 3538 Planarity : 0.004 0.067 3341 Dihedral : 21.250 121.075 9650 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.29 % Allowed : 2.26 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.14), residues: 2285 helix: -2.64 (0.20), residues: 370 sheet: -2.93 (0.18), residues: 517 loop : -3.21 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.012 0.001 HIS E 105 PHE 0.013 0.001 PHE L 49 TYR 0.012 0.001 TYR B 643 ARG 0.003 0.000 ARG C 216 *********************** 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 fitting. rotamer outliers: 6 poor density : 284 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8828 (mt) cc_final: 0.8352 (tp) REVERT: A 382 PHE cc_start: 0.8448 (m-80) cc_final: 0.8050 (m-80) REVERT: A 504 ARG cc_start: 0.3644 (ttm-80) cc_final: 0.2816 (ptm160) REVERT: B 589 ASP cc_start: 0.8422 (t0) cc_final: 0.8172 (t0) REVERT: C 382 PHE cc_start: 0.7057 (m-80) cc_final: 0.6596 (m-80) REVERT: D 541 VAL cc_start: 0.7128 (t) cc_final: 0.6854 (m) REVERT: D 645 LEU cc_start: 0.9283 (mt) cc_final: 0.9075 (pp) REVERT: E 352 TYR cc_start: 0.4459 (p90) cc_final: 0.3987 (p90) REVERT: E 382 PHE cc_start: 0.7498 (m-80) cc_final: 0.6829 (m-80) REVERT: H 34 MET cc_start: 0.6868 (mmm) cc_final: 0.6410 (mmp) outliers start: 6 outliers final: 4 residues processed: 289 average time/residue: 0.3430 time to fit residues: 147.1919 Evaluate side-chains 158 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 249 HIS ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN C 440 GLN C 461 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 186 ASN E 287 GLN E 344 GLN E 478 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 20344 Z= 0.415 Angle : 1.044 21.818 27652 Z= 0.480 Chirality : 0.065 0.557 3538 Planarity : 0.006 0.056 3341 Dihedral : 16.262 109.474 5378 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.90 % Favored : 87.92 % Rotamer: Outliers : 0.74 % Allowed : 9.77 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.15), residues: 2285 helix: -2.00 (0.22), residues: 375 sheet: -2.34 (0.20), residues: 485 loop : -3.03 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 395 HIS 0.022 0.003 HIS A 105 PHE 0.027 0.003 PHE A 210 TYR 0.021 0.002 TYR A 352 ARG 0.007 0.001 ARG A 476 *********************** 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 199 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 2.260 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 95 MET cc_start: 0.8827 (ptt) cc_final: 0.8574 (ptt) REVERT: A 382 PHE cc_start: 0.8504 (m-80) cc_final: 0.8047 (m-80) REVERT: A 504 ARG cc_start: 0.4024 (ttm-80) cc_final: 0.2970 (ptm160) REVERT: B 589 ASP cc_start: 0.8833 (t0) cc_final: 0.8591 (t0) REVERT: B 632 ASP cc_start: 0.7778 (m-30) cc_final: 0.7474 (m-30) REVERT: C 77 THR cc_start: 0.6156 (t) cc_final: 0.5894 (m) REVERT: C 242 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8357 (p) REVERT: C 382 PHE cc_start: 0.7535 (m-10) cc_final: 0.6933 (m-80) REVERT: C 393 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.7994 (p) REVERT: D 588 ARG cc_start: 0.8713 (tpt90) cc_final: 0.8509 (tpp-160) REVERT: E 104 MET cc_start: 0.9146 (ttp) cc_final: 0.8411 (tmm) REVERT: E 271 MET cc_start: 0.7432 (ttm) cc_final: 0.6949 (ttm) REVERT: E 330 HIS cc_start: 0.7985 (m-70) cc_final: 0.7730 (m90) REVERT: E 373 THR cc_start: 0.8136 (t) cc_final: 0.7915 (m) REVERT: E 382 PHE cc_start: 0.7636 (m-80) cc_final: 0.7192 (m-10) REVERT: E 475 MET cc_start: 0.8090 (pmm) cc_final: 0.7085 (pmm) REVERT: H 55 MET cc_start: 0.8206 (mtp) cc_final: 0.7927 (mtm) REVERT: H 95 GLU cc_start: 0.8092 (tt0) cc_final: 0.7722 (pm20) outliers start: 15 outliers final: 2 residues processed: 196 average time/residue: 0.3430 time to fit residues: 100.5629 Evaluate side-chains 122 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 224 optimal weight: 0.0670 chunk 184 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 overall best weight: 2.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN E 72 HIS E 103 GLN E 343 HIS ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20344 Z= 0.268 Angle : 0.873 25.383 27652 Z= 0.401 Chirality : 0.060 0.532 3538 Planarity : 0.005 0.053 3341 Dihedral : 13.593 110.329 5378 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.15), residues: 2285 helix: -1.47 (0.24), residues: 373 sheet: -2.05 (0.21), residues: 473 loop : -2.84 (0.14), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.018 0.002 HIS A 105 PHE 0.017 0.002 PHE L 62 TYR 0.039 0.002 TYR F 643 ARG 0.005 0.001 ARG H 94 *********************** 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 188 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 2.299 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 69 TRP cc_start: 0.5323 (t60) cc_final: 0.4821 (t60) REVERT: A 112 TRP cc_start: 0.6275 (m-10) cc_final: 0.4670 (m-10) REVERT: A 271 MET cc_start: 0.8147 (tpp) cc_final: 0.7865 (tpp) REVERT: A 382 PHE cc_start: 0.8622 (m-80) cc_final: 0.8120 (m-80) REVERT: B 589 ASP cc_start: 0.9102 (t0) cc_final: 0.8870 (t0) REVERT: B 632 ASP cc_start: 0.7761 (m-30) cc_final: 0.7301 (m-30) REVERT: C 150 MET cc_start: 0.5004 (ptt) cc_final: 0.4667 (pmm) REVERT: C 308 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7757 (tpp80) REVERT: C 382 PHE cc_start: 0.7744 (m-10) cc_final: 0.7103 (m-80) REVERT: C 475 MET cc_start: 0.8269 (tmm) cc_final: 0.8049 (tmm) REVERT: D 588 ARG cc_start: 0.8680 (tpt90) cc_final: 0.8435 (tpp-160) REVERT: D 639 THR cc_start: 0.8360 (p) cc_final: 0.8138 (p) REVERT: E 271 MET cc_start: 0.7408 (ttm) cc_final: 0.6847 (ttm) REVERT: E 382 PHE cc_start: 0.7521 (m-80) cc_final: 0.7161 (m-10) REVERT: E 475 MET cc_start: 0.7805 (pmm) cc_final: 0.6578 (pmm) REVERT: H 55 MET cc_start: 0.8110 (mtp) cc_final: 0.7748 (mtm) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.3511 time to fit residues: 98.2058 Evaluate side-chains 119 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.1980 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 0.0770 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 overall best weight: 3.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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** E 377 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20344 Z= 0.293 Angle : 0.868 26.294 27652 Z= 0.401 Chirality : 0.059 0.573 3538 Planarity : 0.005 0.051 3341 Dihedral : 12.064 109.557 5378 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.15), residues: 2285 helix: -1.43 (0.24), residues: 376 sheet: -1.84 (0.22), residues: 444 loop : -2.76 (0.14), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 395 HIS 0.021 0.002 HIS A 105 PHE 0.016 0.002 PHE L 62 TYR 0.034 0.002 TYR B 643 ARG 0.007 0.001 ARG A 340 *********************** 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 171 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 2.000 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 69 TRP cc_start: 0.5325 (t60) cc_final: 0.4726 (t60) REVERT: A 112 TRP cc_start: 0.6398 (m-10) cc_final: 0.4918 (m-10) REVERT: A 252 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8328 (mmm160) REVERT: A 271 MET cc_start: 0.8150 (tpp) cc_final: 0.7950 (tpp) REVERT: A 382 PHE cc_start: 0.8654 (m-80) cc_final: 0.8346 (m-80) REVERT: A 432 GLN cc_start: 0.6702 (pp30) cc_final: 0.6455 (pp30) REVERT: A 435 TYR cc_start: 0.8805 (t80) cc_final: 0.7880 (t80) REVERT: B 589 ASP cc_start: 0.9189 (t0) cc_final: 0.8986 (t0) REVERT: B 626 MET cc_start: 0.5240 (mtt) cc_final: 0.4914 (mtp) REVERT: B 643 TYR cc_start: 0.8754 (m-80) cc_final: 0.8502 (m-80) REVERT: C 150 MET cc_start: 0.4835 (ptt) cc_final: 0.4246 (pmm) REVERT: C 308 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7917 (tpp80) REVERT: C 382 PHE cc_start: 0.7768 (m-10) cc_final: 0.7083 (m-80) REVERT: D 588 ARG cc_start: 0.8695 (tpt90) cc_final: 0.8455 (tpp-160) REVERT: D 591 GLN cc_start: 0.8667 (tp40) cc_final: 0.8230 (tp-100) REVERT: D 626 MET cc_start: 0.4283 (ttp) cc_final: 0.4004 (ttp) REVERT: D 628 TRP cc_start: 0.6826 (t-100) cc_final: 0.6597 (t-100) REVERT: E 271 MET cc_start: 0.7385 (ttm) cc_final: 0.6483 (ttm) REVERT: E 330 HIS cc_start: 0.7913 (m-70) cc_final: 0.7671 (m90) REVERT: E 475 MET cc_start: 0.7958 (pmm) cc_final: 0.6957 (pmm) REVERT: F 601 LYS cc_start: 0.6552 (pttm) cc_final: 0.6176 (tttt) REVERT: F 620 ARG cc_start: 0.7408 (mmp-170) cc_final: 0.6893 (mmp-170) REVERT: F 622 ILE cc_start: 0.8384 (pt) cc_final: 0.8166 (pt) REVERT: H 55 MET cc_start: 0.8210 (mtp) cc_final: 0.7825 (mtm) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.3478 time to fit residues: 89.2796 Evaluate side-chains 117 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 0.0470 chunk 3 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20344 Z= 0.275 Angle : 0.840 22.016 27652 Z= 0.389 Chirality : 0.057 0.521 3538 Planarity : 0.005 0.054 3341 Dihedral : 11.143 108.358 5378 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.16), residues: 2285 helix: -1.32 (0.24), residues: 380 sheet: -1.61 (0.22), residues: 478 loop : -2.69 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 112 HIS 0.018 0.002 HIS A 105 PHE 0.015 0.002 PHE A 391 TYR 0.032 0.002 TYR F 643 ARG 0.007 0.001 ARG A 340 *********************** 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 174 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8354 (tpp) cc_final: 0.7947 (tpp) REVERT: A 337 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8339 (tp-100) REVERT: A 382 PHE cc_start: 0.8654 (m-80) cc_final: 0.8341 (m-80) REVERT: A 435 TYR cc_start: 0.8633 (t80) cc_final: 0.7661 (t80) REVERT: B 626 MET cc_start: 0.5090 (mtt) cc_final: 0.4829 (mtp) REVERT: B 643 TYR cc_start: 0.8554 (m-80) cc_final: 0.8289 (m-80) REVERT: C 150 MET cc_start: 0.5577 (ptt) cc_final: 0.5024 (pmm) REVERT: C 308 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7828 (tpp80) REVERT: C 382 PHE cc_start: 0.7806 (m-10) cc_final: 0.7127 (m-80) REVERT: D 530 MET cc_start: 0.7319 (mmp) cc_final: 0.6369 (mpp) REVERT: D 588 ARG cc_start: 0.8721 (tpt90) cc_final: 0.8512 (tpp-160) REVERT: D 626 MET cc_start: 0.4511 (ttp) cc_final: 0.3694 (ttp) REVERT: D 628 TRP cc_start: 0.7118 (t-100) cc_final: 0.6604 (t-100) REVERT: E 136 THR cc_start: 0.7563 (p) cc_final: 0.7242 (p) REVERT: E 271 MET cc_start: 0.7394 (ttm) cc_final: 0.6475 (ttm) REVERT: E 330 HIS cc_start: 0.7772 (m-70) cc_final: 0.7509 (m90) REVERT: E 382 PHE cc_start: 0.7715 (m-10) cc_final: 0.7075 (m-10) REVERT: E 475 MET cc_start: 0.7924 (pmm) cc_final: 0.7182 (pmm) REVERT: F 544 LEU cc_start: 0.7934 (mt) cc_final: 0.7558 (tt) REVERT: F 601 LYS cc_start: 0.6723 (pttm) cc_final: 0.6327 (mttt) REVERT: F 620 ARG cc_start: 0.7414 (mmp-170) cc_final: 0.6908 (mmp-170) REVERT: H 55 MET cc_start: 0.8302 (mtp) cc_final: 0.7874 (mtm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3454 time to fit residues: 91.0484 Evaluate side-chains 125 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 10.0000 chunk 198 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 220 optimal weight: 40.0000 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 428 GLN E 397 HIS ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 20344 Z= 0.326 Angle : 0.895 26.608 27652 Z= 0.415 Chirality : 0.058 0.520 3538 Planarity : 0.005 0.048 3341 Dihedral : 10.927 107.581 5378 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.16), residues: 2285 helix: -1.47 (0.24), residues: 372 sheet: -1.65 (0.22), residues: 480 loop : -2.63 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 395 HIS 0.019 0.002 HIS A 105 PHE 0.016 0.002 PHE L 62 TYR 0.038 0.002 TYR A 352 ARG 0.011 0.001 ARG C 340 *********************** 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 165 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.192 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 161 MET cc_start: 0.7122 (tpt) cc_final: 0.6679 (tmm) REVERT: A 271 MET cc_start: 0.8539 (tpp) cc_final: 0.6898 (mmt) REVERT: A 382 PHE cc_start: 0.8217 (m-80) cc_final: 0.7904 (m-80) REVERT: A 432 GLN cc_start: 0.6918 (pp30) cc_final: 0.6187 (pp30) REVERT: A 435 TYR cc_start: 0.8664 (t80) cc_final: 0.7609 (t80) REVERT: A 504 ARG cc_start: 0.3334 (ttm-80) cc_final: 0.2711 (ptm160) REVERT: B 589 ASP cc_start: 0.9286 (t0) cc_final: 0.9086 (t0) REVERT: B 590 GLN cc_start: 0.6076 (mp10) cc_final: 0.5829 (tp40) REVERT: B 643 TYR cc_start: 0.8456 (m-80) cc_final: 0.7971 (m-80) REVERT: C 308 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7931 (tpp80) REVERT: C 382 PHE cc_start: 0.7693 (m-10) cc_final: 0.6980 (m-80) REVERT: D 530 MET cc_start: 0.7306 (mmp) cc_final: 0.6057 (mpp) REVERT: D 588 ARG cc_start: 0.8834 (tpt90) cc_final: 0.8591 (tpp-160) REVERT: D 626 MET cc_start: 0.4582 (ttp) cc_final: 0.3581 (ttp) REVERT: D 628 TRP cc_start: 0.7273 (t-100) cc_final: 0.6901 (t-100) REVERT: E 271 MET cc_start: 0.7402 (ttm) cc_final: 0.6611 (ttm) REVERT: E 330 HIS cc_start: 0.7971 (m-70) cc_final: 0.7737 (m90) REVERT: E 382 PHE cc_start: 0.7985 (m-10) cc_final: 0.7304 (m-10) REVERT: E 475 MET cc_start: 0.8049 (pmm) cc_final: 0.7674 (pmm) REVERT: F 544 LEU cc_start: 0.7973 (mt) cc_final: 0.7618 (tt) REVERT: F 601 LYS cc_start: 0.6854 (pttm) cc_final: 0.6567 (mttt) REVERT: F 626 MET cc_start: 0.7070 (ttm) cc_final: 0.6370 (ttm) REVERT: F 643 TYR cc_start: 0.8958 (m-80) cc_final: 0.8656 (m-80) REVERT: H 55 MET cc_start: 0.8407 (mtp) cc_final: 0.7999 (mtm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3275 time to fit residues: 83.2370 Evaluate side-chains 121 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN E 287 GLN ** F 551 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 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 20344 Z= 0.471 Angle : 1.062 23.620 27652 Z= 0.501 Chirality : 0.063 0.560 3538 Planarity : 0.006 0.079 3341 Dihedral : 11.826 107.963 5378 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.15), residues: 2285 helix: -1.96 (0.23), residues: 357 sheet: -1.91 (0.21), residues: 521 loop : -2.82 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP B 628 HIS 0.016 0.002 HIS A 105 PHE 0.028 0.003 PHE A 210 TYR 0.033 0.003 TYR A 352 ARG 0.013 0.001 ARG A 298 *********************** 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 153 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9293 (mt) cc_final: 0.9084 (mt) REVERT: A 161 MET cc_start: 0.7441 (tpt) cc_final: 0.6753 (tmm) REVERT: A 188 ASN cc_start: 0.1315 (p0) cc_final: 0.0962 (p0) REVERT: A 271 MET cc_start: 0.8652 (tpp) cc_final: 0.7239 (mmm) REVERT: A 382 PHE cc_start: 0.8209 (m-80) cc_final: 0.7557 (m-80) REVERT: A 435 TYR cc_start: 0.8655 (t80) cc_final: 0.7589 (t80) REVERT: A 504 ARG cc_start: 0.3245 (ttm-80) cc_final: 0.2645 (ptm160) REVERT: B 643 TYR cc_start: 0.8465 (m-80) cc_final: 0.8089 (m-80) REVERT: C 52 LEU cc_start: 0.8908 (mt) cc_final: 0.8707 (mt) REVERT: C 77 THR cc_start: 0.7551 (t) cc_final: 0.7165 (m) REVERT: C 382 PHE cc_start: 0.7933 (m-10) cc_final: 0.7242 (m-80) REVERT: C 408 MET cc_start: 0.5280 (mtt) cc_final: 0.4696 (mtt) REVERT: D 588 ARG cc_start: 0.8848 (tpt90) cc_final: 0.8466 (tpp-160) REVERT: D 591 GLN cc_start: 0.8928 (tp40) cc_final: 0.8512 (tp40) REVERT: D 626 MET cc_start: 0.4970 (ttp) cc_final: 0.4454 (ttp) REVERT: E 271 MET cc_start: 0.7396 (ttm) cc_final: 0.6560 (ttm) REVERT: E 382 PHE cc_start: 0.7763 (m-10) cc_final: 0.7156 (m-10) REVERT: F 643 TYR cc_start: 0.8935 (m-80) cc_final: 0.8583 (m-80) REVERT: L 1 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7382 (tp-100) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.3383 time to fit residues: 78.7131 Evaluate side-chains 110 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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** B 652 GLN C 103 GLN D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** F 551 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 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20344 Z= 0.280 Angle : 0.898 23.901 27652 Z= 0.416 Chirality : 0.058 0.515 3538 Planarity : 0.005 0.057 3341 Dihedral : 10.928 107.599 5378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.16), residues: 2285 helix: -1.55 (0.23), residues: 370 sheet: -1.71 (0.22), residues: 499 loop : -2.68 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 628 HIS 0.017 0.002 HIS E 105 PHE 0.025 0.002 PHE L 62 TYR 0.026 0.002 TYR E 352 ARG 0.006 0.001 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.467 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 271 MET cc_start: 0.8530 (tpp) cc_final: 0.7039 (mmm) REVERT: A 382 PHE cc_start: 0.8035 (m-80) cc_final: 0.7329 (m-80) REVERT: A 435 TYR cc_start: 0.8643 (t80) cc_final: 0.7640 (t80) REVERT: A 504 ARG cc_start: 0.3696 (ttm-80) cc_final: 0.2695 (ptm160) REVERT: B 590 GLN cc_start: 0.6689 (mp10) cc_final: 0.6446 (mp10) REVERT: C 308 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7678 (tpp80) REVERT: C 382 PHE cc_start: 0.7869 (m-10) cc_final: 0.7208 (m-80) REVERT: D 530 MET cc_start: 0.7097 (mmp) cc_final: 0.6735 (mmm) REVERT: D 589 ASP cc_start: 0.8956 (m-30) cc_final: 0.8746 (m-30) REVERT: D 626 MET cc_start: 0.4537 (ttp) cc_final: 0.3482 (ttp) REVERT: E 271 MET cc_start: 0.7342 (ttm) cc_final: 0.6479 (ttm) REVERT: E 382 PHE cc_start: 0.8063 (m-10) cc_final: 0.7403 (m-10) REVERT: E 468 PHE cc_start: 0.8043 (m-10) cc_final: 0.7824 (m-10) REVERT: F 544 LEU cc_start: 0.7809 (mt) cc_final: 0.7442 (tt) REVERT: F 643 TYR cc_start: 0.9015 (m-80) cc_final: 0.8625 (m-80) REVERT: H 55 MET cc_start: 0.8238 (mtp) cc_final: 0.7945 (mtt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3439 time to fit residues: 81.7082 Evaluate side-chains 124 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 30.0000 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188AASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN F 607 ASN H 1 GLN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN L 126 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20344 Z= 0.344 Angle : 0.943 27.397 27652 Z= 0.438 Chirality : 0.059 0.518 3538 Planarity : 0.005 0.046 3341 Dihedral : 11.059 107.664 5378 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 0.15 % Allowed : 1.13 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.16), residues: 2285 helix: -1.65 (0.23), residues: 364 sheet: -1.86 (0.21), residues: 534 loop : -2.64 (0.15), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 628 HIS 0.017 0.002 HIS E 105 PHE 0.025 0.002 PHE L 62 TYR 0.030 0.002 TYR B 643 ARG 0.012 0.001 ARG C 340 *********************** 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 153 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9188 (mt) cc_final: 0.8897 (mt) REVERT: A 161 MET cc_start: 0.7506 (tpt) cc_final: 0.6822 (tmm) REVERT: A 271 MET cc_start: 0.8498 (tpp) cc_final: 0.7087 (mmm) REVERT: A 382 PHE cc_start: 0.7568 (m-80) cc_final: 0.7338 (m-80) REVERT: A 435 TYR cc_start: 0.8673 (t80) cc_final: 0.7680 (t80) REVERT: A 504 ARG cc_start: 0.3716 (ttm-80) cc_final: 0.2637 (ptm160) REVERT: B 590 GLN cc_start: 0.6614 (mp10) cc_final: 0.6401 (mp10) REVERT: B 626 MET cc_start: 0.5701 (mtt) cc_final: 0.5353 (mtp) REVERT: B 643 TYR cc_start: 0.8638 (m-80) cc_final: 0.8298 (m-80) REVERT: C 308 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7691 (tpp80) REVERT: C 382 PHE cc_start: 0.7994 (m-10) cc_final: 0.7361 (m-80) REVERT: D 530 MET cc_start: 0.7114 (mmp) cc_final: 0.6816 (mmm) REVERT: D 626 MET cc_start: 0.4567 (ttp) cc_final: 0.3577 (ttp) REVERT: E 271 MET cc_start: 0.7362 (ttm) cc_final: 0.6589 (ttm) REVERT: E 382 PHE cc_start: 0.7899 (m-10) cc_final: 0.7154 (m-10) REVERT: E 408 MET cc_start: 0.7336 (mtm) cc_final: 0.7119 (ptp) REVERT: F 544 LEU cc_start: 0.8215 (mt) cc_final: 0.7615 (tt) REVERT: F 643 TYR cc_start: 0.9106 (m-80) cc_final: 0.8635 (m-80) REVERT: H 1 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6255 (pp30) REVERT: H 55 MET cc_start: 0.8369 (mtp) cc_final: 0.8058 (mtt) outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.3455 time to fit residues: 80.1215 Evaluate side-chains 117 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 188AASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 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 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20344 Z= 0.280 Angle : 0.909 26.995 27652 Z= 0.421 Chirality : 0.060 0.713 3538 Planarity : 0.005 0.046 3341 Dihedral : 10.725 107.695 5378 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.16), residues: 2285 helix: -1.52 (0.24), residues: 368 sheet: -1.75 (0.21), residues: 531 loop : -2.59 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 112 HIS 0.018 0.002 HIS E 105 PHE 0.016 0.002 PHE L 62 TYR 0.033 0.002 TYR B 643 ARG 0.006 0.001 ARG L 61 ********************** 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 151 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9195 (mt) cc_final: 0.8965 (mt) REVERT: A 161 MET cc_start: 0.7469 (tpt) cc_final: 0.6833 (tmm) REVERT: A 271 MET cc_start: 0.8474 (tpp) cc_final: 0.7034 (mmm) REVERT: A 382 PHE cc_start: 0.7429 (m-80) cc_final: 0.7180 (m-80) REVERT: A 435 TYR cc_start: 0.8685 (t80) cc_final: 0.7726 (t80) REVERT: A 504 ARG cc_start: 0.3854 (ttm-80) cc_final: 0.2966 (ptm160) REVERT: B 626 MET cc_start: 0.5269 (mtt) cc_final: 0.4922 (mtp) REVERT: B 643 TYR cc_start: 0.8567 (m-80) cc_final: 0.8238 (m-80) REVERT: C 308 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7578 (tpp80) REVERT: C 382 PHE cc_start: 0.8033 (m-10) cc_final: 0.7363 (m-80) REVERT: C 479 TRP cc_start: 0.8363 (m-10) cc_final: 0.8158 (m-10) REVERT: D 530 MET cc_start: 0.6956 (mmp) cc_final: 0.6751 (mmm) REVERT: D 626 MET cc_start: 0.4424 (ttp) cc_final: 0.3436 (ttp) REVERT: E 104 MET cc_start: 0.8544 (ppp) cc_final: 0.8340 (ppp) REVERT: E 271 MET cc_start: 0.7204 (ttm) cc_final: 0.6450 (ttm) REVERT: E 293 THR cc_start: 0.7479 (p) cc_final: 0.7269 (t) REVERT: E 382 PHE cc_start: 0.8073 (m-10) cc_final: 0.7403 (m-10) REVERT: F 544 LEU cc_start: 0.8098 (mt) cc_final: 0.7553 (tt) REVERT: F 586 TYR cc_start: 0.9061 (t80) cc_final: 0.8756 (t80) REVERT: F 643 TYR cc_start: 0.9122 (m-80) cc_final: 0.8704 (m-80) REVERT: H 55 MET cc_start: 0.8263 (mtp) cc_final: 0.7995 (mtt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3181 time to fit residues: 74.8586 Evaluate side-chains 118 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 630 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 103 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.076543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.064387 restraints weight = 143240.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.065753 restraints weight = 96795.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.066710 restraints weight = 72799.194| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20344 Z= 0.252 Angle : 0.892 27.388 27652 Z= 0.412 Chirality : 0.058 0.567 3538 Planarity : 0.005 0.046 3341 Dihedral : 10.350 107.295 5378 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.16), residues: 2285 helix: -1.29 (0.24), residues: 369 sheet: -1.77 (0.21), residues: 540 loop : -2.49 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.003 TRP B 628 HIS 0.022 0.002 HIS A 105 PHE 0.015 0.002 PHE L 62 TYR 0.034 0.002 TYR B 643 ARG 0.006 0.001 ARG E 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.80 seconds wall clock time: 60 minutes 14.99 seconds (3614.99 seconds total)