Starting phenix.real_space_refine on Sun Mar 17 05:23:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/03_2024/7t77_25736_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/03_2024/7t77_25736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/03_2024/7t77_25736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/03_2024/7t77_25736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/03_2024/7t77_25736_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/03_2024/7t77_25736_updated.pdb" } resolution = 4.75 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= 0.010 sd= 0.100 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 105 5.16 5 C 10473 2.51 5 N 2801 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1077 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 9.02, per 1000 atoms: 0.54 Number of scatterers: 16832 At special positions: 0 Unit cell: (129.95, 125.35, 165.6, 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 105 16.00 O 3453 8.00 N 2801 7.00 C 10473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.14 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.08 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.16 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 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 L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA h 3 " - " MAN h 7 " " MAN h 4 " - " MAN h 5 " " BMA j 3 " - " MAN j 6 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 6 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 130 " " NAG A 607 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 185h" " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 448 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 130 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 301 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN E 448 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN E 130 " " NAG j 1 " - " ASN E 156 " Time building additional restraints: 7.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 34 sheets defined 21.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.680A pdb=" N LEU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.828A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.511A pdb=" N GLN B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 662 removed outlier: 5.057A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER B 649 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN B 651 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLN B 652 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 655 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 661 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.733A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 475 through 478 Processing helix chain 'C' and resid 482 through 485 removed outlier: 4.165A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 485' Processing helix chain 'D' and resid 532 through 543 removed outlier: 5.141A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 660 removed outlier: 5.120A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 642 " --> pdb=" O THR D 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 648 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 649 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 650 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 651 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 652 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 654 " --> pdb=" O ASN D 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 336 through 339 No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 341 through 351 removed outlier: 3.694A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 475 through 485 removed outlier: 4.664A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 538 through 544 removed outlier: 3.790A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 649 removed outlier: 5.671A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 661 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.685A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 304 through 308 Processing sheet with id= J, first strand: chain 'A' and resid 423 through 425 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= M, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= N, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.758A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= P, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.345A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.728A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 423 through 425 Processing sheet with id= T, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.601A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= V, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= W, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'E' and resid 129 through 133 Processing sheet with id= Y, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= Z, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= AA, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.388A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.629A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AD, first strand: chain 'H' and resid 107 through 109 removed outlier: 6.040A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.873A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.022A pdb=" N LYS L 103 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= AH, first strand: chain 'L' and resid 96 through 98 removed outlier: 5.858A pdb=" N GLN L 37 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1227 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: 5.67 Time building geometry restraints manager: 8.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 3357 1.32 - 1.47: 6058 1.47 - 1.61: 7591 1.61 - 1.76: 23 1.76 - 1.91: 127 Bond restraints: 17156 Sorted by residual: bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.53e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CB LEU L 106A" pdb=" CG LEU L 106A" ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NE ARG H 3 " pdb=" CZ ARG H 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 96.66 - 109.57: 3998 109.57 - 122.47: 16487 122.47 - 135.38: 2808 135.38 - 148.29: 0 148.29 - 161.19: 3 Bond angle restraints: 23296 Sorted by residual: angle pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " pdb=" C7 NAG A 601 " ideal model delta sigma weight residual 124.56 161.19 -36.63 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C2 NAG E 605 " pdb=" N2 NAG E 605 " pdb=" C7 NAG E 605 " ideal model delta sigma weight residual 124.56 160.59 -36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 159.61 -35.05 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C HIS E 72 " pdb=" N ALA E 73 " pdb=" CA ALA E 73 " ideal model delta sigma weight residual 122.84 109.29 13.55 1.30e+00 5.92e-01 1.09e+02 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.85 128.36 -8.51 1.01e+00 9.80e-01 7.10e+01 ... (remaining 23291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 11169 21.61 - 43.21: 278 43.21 - 64.82: 86 64.82 - 86.43: 71 86.43 - 108.04: 33 Dihedral angle restraints: 11637 sinusoidal: 5999 harmonic: 5638 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 149.44 -56.44 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual 93.00 142.47 -49.47 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 11634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1855 0.107 - 0.214: 642 0.214 - 0.321: 242 0.321 - 0.428: 112 0.428 - 0.535: 62 Chirality restraints: 2913 Sorted by residual: chirality pdb=" C1 MAN R 5 " pdb=" O6 BMA R 3 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.36e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.68e+02 ... (remaining 2910 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG i 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG j 2 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.526 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG j 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.210 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4251 2.82 - 3.34: 15810 3.34 - 3.86: 28353 3.86 - 4.38: 34182 4.38 - 4.90: 51975 Nonbonded interactions: 134571 Sorted by model distance: nonbonded pdb=" O TRP E 69 " pdb=" N THR E 71 " model vdw 2.295 2.520 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS F 574 " model vdw 2.388 2.520 nonbonded pdb=" N GLY A 41 " pdb=" N VAL A 42 " model vdw 2.415 2.560 nonbonded pdb=" N LYS E 97 " pdb=" N ASN E 98 " model vdw 2.418 2.560 nonbonded pdb=" N ASP C 141 " pdb=" OD1 ASP C 141 " model vdw 2.441 2.520 ... (remaining 134566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 502 or resid 601 through 607)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'i' } ncs_group { reference = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'j' and (resid 1 or resid 4 through 6)) } 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.510 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.300 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.022 0.136 17156 Z= 1.401 Angle : 1.828 36.634 23296 Z= 1.161 Chirality : 0.153 0.535 2913 Planarity : 0.016 0.304 2833 Dihedral : 13.668 108.037 7897 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.71 % Favored : 97.03 % Rotamer: Outliers : 0.87 % Allowed : 0.93 % Favored : 98.20 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1918 helix: -0.47 (0.23), residues: 417 sheet: 0.70 (0.21), residues: 558 loop : 0.50 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.008 TRP E 479 HIS 0.010 0.002 HIS A 374 PHE 0.045 0.007 PHE C 93 TYR 0.054 0.008 TYR C 40 ARG 0.010 0.001 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 392 time to evaluate : 2.003 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: A 111 LEU cc_start: 0.9519 (mt) cc_final: 0.9049 (tp) REVERT: A 180 ASP cc_start: 0.8734 (m-30) cc_final: 0.8443 (m-30) REVERT: A 271 ILE cc_start: 0.9434 (mt) cc_final: 0.9209 (tp) REVERT: A 423 ILE cc_start: 0.9118 (mt) cc_final: 0.8755 (mm) REVERT: B 528 SER cc_start: 0.8591 (m) cc_final: 0.7830 (t) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8383 (mtm) REVERT: B 584 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8939 (tp30) REVERT: B 647 GLU cc_start: 0.8993 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 651 ASN cc_start: 0.8977 (m-40) cc_final: 0.8690 (p0) REVERT: B 654 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7934 (tm-30) REVERT: C 53 PHE cc_start: 0.7879 (m-80) cc_final: 0.7627 (m-10) REVERT: C 101 VAL cc_start: 0.9492 (t) cc_final: 0.9286 (p) REVERT: C 383 PHE cc_start: 0.9129 (m-80) cc_final: 0.8804 (m-80) REVERT: C 384 TYR cc_start: 0.8917 (m-80) cc_final: 0.8440 (m-80) REVERT: C 424 ILE cc_start: 0.8785 (mt) cc_final: 0.8583 (mm) REVERT: D 536 THR cc_start: 0.9269 (p) cc_final: 0.8962 (t) REVERT: D 538 THR cc_start: 0.9005 (p) cc_final: 0.7872 (p) REVERT: D 650 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7904 (tp40) REVERT: E 42 VAL cc_start: 0.9085 (t) cc_final: 0.8673 (t) REVERT: E 69 TRP cc_start: 0.8678 (m-90) cc_final: 0.8294 (m-90) REVERT: E 87 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 98 ASN cc_start: 0.9228 (t0) cc_final: 0.8431 (t0) REVERT: E 254 VAL cc_start: 0.9475 (t) cc_final: 0.9233 (p) REVERT: F 530 MET cc_start: 0.9365 (mtp) cc_final: 0.9047 (mtp) REVERT: F 535 MET cc_start: 0.9067 (mmp) cc_final: 0.8619 (tpp) REVERT: F 540 GLN cc_start: 0.8731 (mm110) cc_final: 0.8004 (mt0) REVERT: F 573 ILE cc_start: 0.8643 (mt) cc_final: 0.8334 (mm) REVERT: F 574 LYS cc_start: 0.8958 (mttt) cc_final: 0.8475 (mtmt) REVERT: F 584 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8871 (tp30) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9346 (mmmt) REVERT: F 643 TYR cc_start: 0.9363 (m-10) cc_final: 0.9009 (m-80) REVERT: F 648 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8551 (tt0) REVERT: F 660 LEU cc_start: 0.8323 (mt) cc_final: 0.8029 (mt) REVERT: H 28 ASP cc_start: 0.8808 (t0) cc_final: 0.8297 (t0) REVERT: H 67 LEU cc_start: 0.8266 (mt) cc_final: 0.8016 (mm) REVERT: H 78 LEU cc_start: 0.9286 (tp) cc_final: 0.9046 (tp) REVERT: H 82 MET cc_start: 0.9002 (ptp) cc_final: 0.8520 (ttt) REVERT: H 91 PHE cc_start: 0.9263 (m-80) cc_final: 0.8933 (m-80) REVERT: L 4 LEU cc_start: 0.8996 (mt) cc_final: 0.8675 (tt) REVERT: L 36 TYR cc_start: 0.8280 (m-80) cc_final: 0.7911 (m-80) REVERT: L 69 ASN cc_start: 0.8219 (m-40) cc_final: 0.7683 (m-40) REVERT: L 78 LEU cc_start: 0.8730 (tp) cc_final: 0.8527 (tt) REVERT: L 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7463 (m-30) REVERT: L 88 CYS cc_start: 0.3702 (p) cc_final: 0.3100 (p) REVERT: L 96 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8662 (mmt90) outliers start: 15 outliers final: 6 residues processed: 406 average time/residue: 0.2993 time to fit residues: 176.3935 Evaluate side-chains 207 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 302 ASN D 543 ASN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN E 195 ASN F 543 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17156 Z= 0.230 Angle : 0.757 14.239 23296 Z= 0.384 Chirality : 0.050 0.403 2913 Planarity : 0.005 0.046 2833 Dihedral : 11.203 81.838 4264 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.17 % Allowed : 2.03 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1918 helix: 0.40 (0.26), residues: 366 sheet: 0.43 (0.21), residues: 559 loop : 0.13 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.011 0.001 HIS A 190 PHE 0.022 0.002 PHE A 233 TYR 0.037 0.002 TYR C 484 ARG 0.008 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 1.714 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: A 111 LEU cc_start: 0.9452 (mt) cc_final: 0.9097 (tp) REVERT: A 180 ASP cc_start: 0.8913 (m-30) cc_final: 0.8140 (m-30) REVERT: A 201 ILE cc_start: 0.9338 (mp) cc_final: 0.8775 (tp) REVERT: A 423 ILE cc_start: 0.8951 (mt) cc_final: 0.8495 (mm) REVERT: A 425 ASN cc_start: 0.8494 (p0) cc_final: 0.8135 (p0) REVERT: A 491 ILE cc_start: 0.9198 (tp) cc_final: 0.8835 (tp) REVERT: B 528 SER cc_start: 0.8708 (m) cc_final: 0.7958 (t) REVERT: B 655 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8773 (tptt) REVERT: B 657 GLU cc_start: 0.9346 (mp0) cc_final: 0.9093 (mp0) REVERT: C 186 ARG cc_start: 0.7920 (mmp80) cc_final: 0.7376 (ptm160) REVERT: C 217 TYR cc_start: 0.7229 (m-10) cc_final: 0.6933 (m-10) REVERT: C 384 TYR cc_start: 0.8531 (m-80) cc_final: 0.8061 (m-80) REVERT: C 434 MET cc_start: 0.7928 (ppp) cc_final: 0.7710 (ppp) REVERT: C 489 VAL cc_start: 0.9026 (m) cc_final: 0.8813 (t) REVERT: D 538 THR cc_start: 0.8683 (p) cc_final: 0.8443 (p) REVERT: D 584 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8890 (tp30) REVERT: D 591 GLN cc_start: 0.9160 (mm110) cc_final: 0.8800 (mm110) REVERT: D 650 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7651 (mm110) REVERT: E 42 VAL cc_start: 0.8869 (t) cc_final: 0.8668 (t) REVERT: E 69 TRP cc_start: 0.8377 (m-90) cc_final: 0.7914 (m-10) REVERT: E 98 ASN cc_start: 0.9323 (t0) cc_final: 0.8177 (t0) REVERT: E 434 MET cc_start: 0.8688 (mtp) cc_final: 0.8468 (mtp) REVERT: E 483 LEU cc_start: 0.8924 (mt) cc_final: 0.7872 (mt) REVERT: F 530 MET cc_start: 0.9278 (mtp) cc_final: 0.8966 (mtp) REVERT: F 535 MET cc_start: 0.9005 (mmp) cc_final: 0.8407 (tpp) REVERT: F 570 HIS cc_start: 0.7548 (p-80) cc_final: 0.7343 (p90) REVERT: F 584 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8964 (tp30) REVERT: F 633 LYS cc_start: 0.9710 (mttt) cc_final: 0.9330 (mmmt) REVERT: F 654 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8736 (mm-30) REVERT: H 12 VAL cc_start: 0.8627 (m) cc_final: 0.8322 (m) REVERT: H 28 ASP cc_start: 0.8853 (t0) cc_final: 0.8542 (t70) REVERT: H 45 LEU cc_start: 0.9075 (mm) cc_final: 0.8692 (mm) REVERT: H 53 ASP cc_start: 0.8738 (p0) cc_final: 0.8396 (p0) REVERT: H 78 LEU cc_start: 0.9233 (tp) cc_final: 0.8933 (tp) REVERT: H 82 ASN cc_start: 0.8208 (m-40) cc_final: 0.7909 (p0) REVERT: H 100 MET cc_start: 0.9315 (mpp) cc_final: 0.8804 (mpp) REVERT: L 36 TYR cc_start: 0.8293 (m-80) cc_final: 0.6763 (m-80) REVERT: L 50 ASP cc_start: 0.7986 (m-30) cc_final: 0.7402 (m-30) REVERT: L 69 ASN cc_start: 0.8257 (m-40) cc_final: 0.7809 (m110) REVERT: L 70 THR cc_start: 0.8707 (m) cc_final: 0.8491 (p) REVERT: L 86 TYR cc_start: 0.8509 (m-80) cc_final: 0.8177 (m-80) REVERT: L 89 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8876 (ttpt) REVERT: L 104 LEU cc_start: 0.8712 (tt) cc_final: 0.8330 (tt) outliers start: 3 outliers final: 1 residues processed: 270 average time/residue: 0.2555 time to fit residues: 107.2646 Evaluate side-chains 180 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 478 ASN B 585 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS D 585 HIS D 590 GLN D 607 ASN D 625 ASN D 650 GLN D 651 ASN E 374 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100RHIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17156 Z= 0.291 Angle : 0.731 9.378 23296 Z= 0.369 Chirality : 0.048 0.358 2913 Planarity : 0.005 0.046 2833 Dihedral : 8.944 73.744 4264 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.23 % Allowed : 1.92 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1918 helix: 0.22 (0.27), residues: 366 sheet: 0.31 (0.21), residues: 567 loop : -0.26 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 571 HIS 0.006 0.002 HIS A 190 PHE 0.017 0.002 PHE C 53 TYR 0.019 0.002 TYR L 87 ARG 0.006 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 1.961 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 180 ASP cc_start: 0.8907 (m-30) cc_final: 0.8024 (m-30) REVERT: A 201 ILE cc_start: 0.9500 (mp) cc_final: 0.8971 (tp) REVERT: A 423 ILE cc_start: 0.9055 (mt) cc_final: 0.8676 (mm) REVERT: A 425 ASN cc_start: 0.8476 (p0) cc_final: 0.8096 (p0) REVERT: A 434 MET cc_start: 0.8795 (tpp) cc_final: 0.8431 (tpp) REVERT: B 626 MET cc_start: 0.8768 (mmp) cc_final: 0.8147 (mmm) REVERT: B 655 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8631 (tptm) REVERT: B 657 GLU cc_start: 0.9335 (mp0) cc_final: 0.9051 (mp0) REVERT: C 52 LEU cc_start: 0.9436 (mt) cc_final: 0.9214 (mp) REVERT: C 150 MET cc_start: 0.9054 (mmp) cc_final: 0.8722 (mmm) REVERT: C 186 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7163 (ptm160) REVERT: D 584 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8971 (tp30) REVERT: D 626 MET cc_start: 0.9300 (tpp) cc_final: 0.8931 (tpp) REVERT: D 650 GLN cc_start: 0.8270 (mm110) cc_final: 0.7819 (mm-40) REVERT: E 69 TRP cc_start: 0.8365 (m-90) cc_final: 0.8011 (m-90) REVERT: E 434 MET cc_start: 0.9155 (mtm) cc_final: 0.8800 (mtm) REVERT: F 530 MET cc_start: 0.9194 (mtp) cc_final: 0.8912 (ttm) REVERT: F 535 MET cc_start: 0.9045 (mmp) cc_final: 0.8326 (tpp) REVERT: F 584 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8876 (tp30) REVERT: F 601 LYS cc_start: 0.9281 (mttt) cc_final: 0.8746 (mtmt) REVERT: F 633 LYS cc_start: 0.9697 (mttt) cc_final: 0.9348 (mmmt) REVERT: F 654 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8768 (mm-30) REVERT: H 28 ASP cc_start: 0.9066 (t0) cc_final: 0.7953 (p0) REVERT: H 32 GLN cc_start: 0.9225 (mp10) cc_final: 0.8686 (mp10) REVERT: H 45 LEU cc_start: 0.8875 (mm) cc_final: 0.8362 (mm) REVERT: H 53 ASP cc_start: 0.8854 (p0) cc_final: 0.8492 (p0) REVERT: H 78 LEU cc_start: 0.9278 (tp) cc_final: 0.8991 (tp) REVERT: H 82 MET cc_start: 0.8994 (ttt) cc_final: 0.8514 (tpt) REVERT: H 100 MET cc_start: 0.9421 (mpp) cc_final: 0.9084 (mpp) REVERT: L 88 CYS cc_start: 0.5770 (p) cc_final: 0.5281 (p) REVERT: L 89 LYS cc_start: 0.9176 (ttpp) cc_final: 0.8837 (ttpt) outliers start: 4 outliers final: 2 residues processed: 208 average time/residue: 0.2533 time to fit residues: 82.7602 Evaluate side-chains 145 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN B 650 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 114 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17156 Z= 0.185 Angle : 0.621 9.828 23296 Z= 0.313 Chirality : 0.047 0.318 2913 Planarity : 0.004 0.063 2833 Dihedral : 7.904 68.989 4264 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 1918 helix: 0.17 (0.27), residues: 366 sheet: 0.23 (0.22), residues: 551 loop : -0.29 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 96 HIS 0.005 0.001 HIS A 249 PHE 0.014 0.001 PHE E 383 TYR 0.012 0.001 TYR E 217 ARG 0.012 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.782 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 180 ASP cc_start: 0.8743 (m-30) cc_final: 0.7847 (m-30) REVERT: A 201 ILE cc_start: 0.9521 (mp) cc_final: 0.8928 (tp) REVERT: A 260 LEU cc_start: 0.9321 (mp) cc_final: 0.9098 (mp) REVERT: A 423 ILE cc_start: 0.8995 (mt) cc_final: 0.8689 (mm) REVERT: A 425 ASN cc_start: 0.8383 (p0) cc_final: 0.8005 (p0) REVERT: B 626 MET cc_start: 0.8434 (mmp) cc_final: 0.7874 (mmm) REVERT: B 642 ILE cc_start: 0.9690 (tp) cc_final: 0.9486 (tp) REVERT: B 654 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9128 (mm-30) REVERT: B 657 GLU cc_start: 0.9305 (mp0) cc_final: 0.8971 (mp0) REVERT: C 104 MET cc_start: 0.9015 (ttm) cc_final: 0.8794 (ttm) REVERT: C 150 MET cc_start: 0.9153 (mmp) cc_final: 0.8830 (mmp) REVERT: C 186 ARG cc_start: 0.7876 (mmp80) cc_final: 0.7234 (ptm160) REVERT: C 383 PHE cc_start: 0.8818 (m-80) cc_final: 0.8551 (m-80) REVERT: D 584 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8949 (tp30) REVERT: D 610 TRP cc_start: 0.6709 (p90) cc_final: 0.6485 (p90) REVERT: D 650 GLN cc_start: 0.8275 (mm110) cc_final: 0.7771 (mm-40) REVERT: E 69 TRP cc_start: 0.8323 (m-90) cc_final: 0.7926 (m-90) REVERT: E 100 MET cc_start: 0.9439 (ptm) cc_final: 0.9192 (ppp) REVERT: E 434 MET cc_start: 0.9124 (mtm) cc_final: 0.8805 (mtm) REVERT: E 483 LEU cc_start: 0.9506 (mt) cc_final: 0.9097 (mt) REVERT: F 530 MET cc_start: 0.9262 (mtp) cc_final: 0.8914 (ttm) REVERT: F 535 MET cc_start: 0.8973 (mmp) cc_final: 0.8356 (tmm) REVERT: F 584 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8866 (tp30) REVERT: F 601 LYS cc_start: 0.9266 (mttt) cc_final: 0.9044 (mtmt) REVERT: F 633 LYS cc_start: 0.9676 (mttt) cc_final: 0.9341 (mmmt) REVERT: F 654 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8714 (mm-30) REVERT: H 28 ASP cc_start: 0.8855 (t0) cc_final: 0.7975 (p0) REVERT: H 32 GLN cc_start: 0.9156 (mp10) cc_final: 0.8642 (mp10) REVERT: H 53 ASP cc_start: 0.8883 (p0) cc_final: 0.8487 (p0) REVERT: H 75 LYS cc_start: 0.9364 (mtmt) cc_final: 0.9133 (mtmt) REVERT: H 78 LEU cc_start: 0.9265 (tp) cc_final: 0.8933 (tp) REVERT: H 82 MET cc_start: 0.8882 (ttt) cc_final: 0.8420 (tpt) REVERT: H 100 MET cc_start: 0.9326 (mpp) cc_final: 0.9119 (mpp) REVERT: L 35 TRP cc_start: 0.8367 (m100) cc_final: 0.7985 (m100) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2621 time to fit residues: 81.3354 Evaluate side-chains 151 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 158 optimal weight: 0.3980 chunk 128 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17156 Z= 0.307 Angle : 0.701 9.384 23296 Z= 0.356 Chirality : 0.047 0.329 2913 Planarity : 0.005 0.050 2833 Dihedral : 7.740 67.114 4264 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1918 helix: -0.27 (0.26), residues: 375 sheet: -0.03 (0.21), residues: 561 loop : -0.57 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 628 HIS 0.008 0.001 HIS C 85 PHE 0.015 0.002 PHE A 233 TYR 0.016 0.002 TYR A 217 ARG 0.006 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8210 (m-10) cc_final: 0.7987 (m-10) REVERT: A 98 ASN cc_start: 0.9484 (t0) cc_final: 0.9268 (t0) REVERT: A 150 MET cc_start: 0.8139 (ptp) cc_final: 0.7922 (ptp) REVERT: A 201 ILE cc_start: 0.9526 (mp) cc_final: 0.9114 (tp) REVERT: A 425 ASN cc_start: 0.8251 (p0) cc_final: 0.7723 (p0) REVERT: B 626 MET cc_start: 0.8779 (mmp) cc_final: 0.8352 (mmm) REVERT: C 104 MET cc_start: 0.9107 (ttm) cc_final: 0.8905 (ttm) REVERT: C 150 MET cc_start: 0.9196 (mmp) cc_final: 0.8814 (mmp) REVERT: C 186 ARG cc_start: 0.7879 (mmp80) cc_final: 0.7255 (ptm160) REVERT: C 434 MET cc_start: 0.8143 (ppp) cc_final: 0.7894 (ppp) REVERT: D 626 MET cc_start: 0.9564 (mmp) cc_final: 0.9265 (tpp) REVERT: E 69 TRP cc_start: 0.8387 (m-90) cc_final: 0.8179 (m-90) REVERT: E 100 MET cc_start: 0.9603 (ptm) cc_final: 0.9264 (ppp) REVERT: E 104 MET cc_start: 0.9469 (mmt) cc_final: 0.9247 (mmt) REVERT: E 279 ASN cc_start: 0.8927 (t0) cc_final: 0.8217 (t0) REVERT: E 434 MET cc_start: 0.9254 (mtm) cc_final: 0.8882 (mtm) REVERT: F 530 MET cc_start: 0.9259 (mtp) cc_final: 0.8997 (mtt) REVERT: F 601 LYS cc_start: 0.9492 (mttt) cc_final: 0.9198 (mtmt) REVERT: F 626 MET cc_start: 0.8400 (tpp) cc_final: 0.8190 (tpp) REVERT: F 633 LYS cc_start: 0.9688 (mttt) cc_final: 0.9352 (mmmt) REVERT: F 654 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8717 (mm-30) REVERT: H 28 ASP cc_start: 0.8845 (t0) cc_final: 0.8496 (m-30) REVERT: H 53 ASP cc_start: 0.8878 (p0) cc_final: 0.8453 (p0) REVERT: H 75 LYS cc_start: 0.9409 (mtmt) cc_final: 0.9151 (mtmt) REVERT: H 78 LEU cc_start: 0.9392 (tp) cc_final: 0.9064 (tp) REVERT: H 82 MET cc_start: 0.8917 (ttt) cc_final: 0.8576 (tpt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2739 time to fit residues: 74.4948 Evaluate side-chains 122 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17156 Z= 0.317 Angle : 0.697 9.333 23296 Z= 0.356 Chirality : 0.047 0.288 2913 Planarity : 0.006 0.228 2833 Dihedral : 7.822 63.209 4264 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1918 helix: -0.46 (0.26), residues: 381 sheet: -0.22 (0.21), residues: 557 loop : -0.79 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 610 HIS 0.007 0.001 HIS C 85 PHE 0.014 0.002 PHE C 53 TYR 0.024 0.002 TYR B 638 ARG 0.015 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8363 (m-10) cc_final: 0.8123 (m-10) REVERT: A 150 MET cc_start: 0.8467 (ptp) cc_final: 0.7934 (ptt) REVERT: A 201 ILE cc_start: 0.9559 (mp) cc_final: 0.9154 (tp) REVERT: A 425 ASN cc_start: 0.8210 (p0) cc_final: 0.7672 (p0) REVERT: A 494 LEU cc_start: 0.8945 (mt) cc_final: 0.8406 (mt) REVERT: B 626 MET cc_start: 0.8717 (mmp) cc_final: 0.8295 (mmm) REVERT: B 642 ILE cc_start: 0.9720 (tp) cc_final: 0.9518 (tt) REVERT: B 647 GLU cc_start: 0.9094 (pp20) cc_final: 0.8874 (pp20) REVERT: B 657 GLU cc_start: 0.9239 (mp0) cc_final: 0.8912 (mp0) REVERT: C 150 MET cc_start: 0.9283 (mmp) cc_final: 0.9052 (mmp) REVERT: C 186 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7484 (ptm160) REVERT: C 434 MET cc_start: 0.8022 (ppp) cc_final: 0.7761 (ppp) REVERT: D 584 GLU cc_start: 0.9339 (tp30) cc_final: 0.9084 (tp30) REVERT: D 626 MET cc_start: 0.9547 (mmp) cc_final: 0.9295 (tpp) REVERT: E 69 TRP cc_start: 0.8340 (m-90) cc_final: 0.7908 (m-90) REVERT: E 100 MET cc_start: 0.9585 (ptm) cc_final: 0.9278 (ppp) REVERT: E 279 ASN cc_start: 0.9066 (t0) cc_final: 0.8422 (t0) REVERT: E 434 MET cc_start: 0.9306 (mtm) cc_final: 0.8780 (mtm) REVERT: F 530 MET cc_start: 0.9313 (mtp) cc_final: 0.8938 (mtt) REVERT: F 626 MET cc_start: 0.8436 (tpp) cc_final: 0.8160 (tpp) REVERT: F 633 LYS cc_start: 0.9702 (mttt) cc_final: 0.9368 (mmmt) REVERT: F 655 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9021 (ttmm) REVERT: H 28 ASP cc_start: 0.8719 (t0) cc_final: 0.8356 (m-30) REVERT: H 53 ASP cc_start: 0.8959 (p0) cc_final: 0.8505 (p0) REVERT: H 75 LYS cc_start: 0.9398 (mtmt) cc_final: 0.9144 (mtmt) REVERT: H 78 LEU cc_start: 0.9364 (tp) cc_final: 0.9023 (tp) REVERT: H 91 PHE cc_start: 0.8999 (m-80) cc_final: 0.8666 (m-80) REVERT: H 100 ASP cc_start: 0.9253 (t0) cc_final: 0.8985 (t0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2560 time to fit residues: 66.4457 Evaluate side-chains 118 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN B 658 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17156 Z= 0.192 Angle : 0.600 9.447 23296 Z= 0.308 Chirality : 0.046 0.256 2913 Planarity : 0.005 0.133 2833 Dihedral : 7.397 60.810 4264 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1918 helix: -0.14 (0.27), residues: 375 sheet: -0.15 (0.22), residues: 542 loop : -0.73 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.006 0.001 HIS A 249 PHE 0.019 0.001 PHE E 383 TYR 0.015 0.001 TYR B 638 ARG 0.011 0.000 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.045 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: A 69 TRP cc_start: 0.8327 (m-10) cc_final: 0.8123 (m-10) REVERT: A 150 MET cc_start: 0.8515 (ptp) cc_final: 0.8067 (ptt) REVERT: A 201 ILE cc_start: 0.9565 (mp) cc_final: 0.9183 (tp) REVERT: A 260 LEU cc_start: 0.9323 (mp) cc_final: 0.9113 (mp) REVERT: A 425 ASN cc_start: 0.8119 (p0) cc_final: 0.7660 (p0) REVERT: A 494 LEU cc_start: 0.8918 (mt) cc_final: 0.8500 (mt) REVERT: B 528 SER cc_start: 0.9407 (m) cc_final: 0.8731 (p) REVERT: B 626 MET cc_start: 0.8662 (mmp) cc_final: 0.8261 (mmm) REVERT: B 647 GLU cc_start: 0.9171 (pp20) cc_final: 0.8969 (pp20) REVERT: B 651 ASN cc_start: 0.9279 (p0) cc_final: 0.8966 (p0) REVERT: B 657 GLU cc_start: 0.9235 (mp0) cc_final: 0.8852 (mp0) REVERT: C 150 MET cc_start: 0.9292 (mmp) cc_final: 0.9064 (mmp) REVERT: C 186 ARG cc_start: 0.7947 (mmp80) cc_final: 0.7510 (ptm160) REVERT: C 434 MET cc_start: 0.8007 (ppp) cc_final: 0.7776 (ppp) REVERT: D 584 GLU cc_start: 0.9287 (tp30) cc_final: 0.9004 (tp30) REVERT: D 626 MET cc_start: 0.9511 (mmp) cc_final: 0.9302 (tpp) REVERT: E 69 TRP cc_start: 0.8192 (m-90) cc_final: 0.7766 (m-90) REVERT: E 100 MET cc_start: 0.9531 (ptm) cc_final: 0.9215 (ppp) REVERT: E 103 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8380 (tp-100) REVERT: E 279 ASN cc_start: 0.8993 (t0) cc_final: 0.8389 (t0) REVERT: E 434 MET cc_start: 0.9277 (mtm) cc_final: 0.8789 (mtm) REVERT: F 530 MET cc_start: 0.9345 (mtp) cc_final: 0.8949 (mtt) REVERT: F 535 MET cc_start: 0.8755 (mmp) cc_final: 0.8423 (tmm) REVERT: F 545 LEU cc_start: 0.9146 (tp) cc_final: 0.8836 (tp) REVERT: F 626 MET cc_start: 0.8455 (tpp) cc_final: 0.8231 (tpp) REVERT: F 633 LYS cc_start: 0.9695 (mttt) cc_final: 0.9347 (mmmt) REVERT: F 655 LYS cc_start: 0.9539 (ttmm) cc_final: 0.9089 (ttmm) REVERT: F 660 LEU cc_start: 0.8628 (tp) cc_final: 0.8408 (pp) REVERT: H 28 ASP cc_start: 0.8613 (t0) cc_final: 0.8238 (m-30) REVERT: H 53 ASP cc_start: 0.8913 (p0) cc_final: 0.8429 (p0) REVERT: H 75 LYS cc_start: 0.9419 (mtmt) cc_final: 0.9135 (mtmt) REVERT: H 78 LEU cc_start: 0.9358 (tp) cc_final: 0.9080 (tp) REVERT: H 82 MET cc_start: 0.8915 (ttt) cc_final: 0.8466 (tpt) REVERT: H 100 ASP cc_start: 0.9163 (t0) cc_final: 0.8859 (t0) REVERT: L 35 TRP cc_start: 0.8414 (m100) cc_final: 0.8070 (m100) REVERT: L 88 CYS cc_start: 0.6823 (t) cc_final: 0.5720 (t) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2589 time to fit residues: 71.3839 Evaluate side-chains 127 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17156 Z= 0.336 Angle : 0.728 9.419 23296 Z= 0.368 Chirality : 0.047 0.285 2913 Planarity : 0.007 0.253 2833 Dihedral : 7.822 60.235 4264 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1918 helix: -0.72 (0.25), residues: 396 sheet: -0.35 (0.23), residues: 496 loop : -1.01 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 427 HIS 0.007 0.002 HIS C 85 PHE 0.015 0.002 PHE E 382 TYR 0.018 0.002 TYR C 484 ARG 0.016 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.031 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: A 69 TRP cc_start: 0.8416 (m-10) cc_final: 0.8140 (m-10) REVERT: A 150 MET cc_start: 0.8478 (ptp) cc_final: 0.8083 (ptt) REVERT: A 425 ASN cc_start: 0.8186 (p0) cc_final: 0.7613 (p0) REVERT: B 528 SER cc_start: 0.9296 (m) cc_final: 0.8746 (p) REVERT: B 626 MET cc_start: 0.8621 (mmp) cc_final: 0.8273 (mmm) REVERT: B 647 GLU cc_start: 0.9162 (pp20) cc_final: 0.8866 (pp20) REVERT: B 651 ASN cc_start: 0.9291 (p0) cc_final: 0.8845 (p0) REVERT: B 657 GLU cc_start: 0.9247 (mp0) cc_final: 0.8836 (mp0) REVERT: C 150 MET cc_start: 0.9295 (mmp) cc_final: 0.8996 (mmp) REVERT: C 381 GLU cc_start: 0.9062 (tp30) cc_final: 0.8548 (tp30) REVERT: E 69 TRP cc_start: 0.8398 (m-90) cc_final: 0.7934 (m-90) REVERT: E 103 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8451 (tp-100) REVERT: E 434 MET cc_start: 0.9006 (mtm) cc_final: 0.8675 (mtm) REVERT: F 530 MET cc_start: 0.9307 (mtp) cc_final: 0.8920 (mtt) REVERT: F 545 LEU cc_start: 0.9284 (tp) cc_final: 0.8983 (tp) REVERT: F 626 MET cc_start: 0.8316 (tpp) cc_final: 0.7953 (tpp) REVERT: F 633 LYS cc_start: 0.9715 (mttt) cc_final: 0.9389 (mmmt) REVERT: F 655 LYS cc_start: 0.9573 (ttmm) cc_final: 0.9079 (ttmm) REVERT: H 18 LEU cc_start: 0.8733 (tp) cc_final: 0.8154 (tp) REVERT: H 53 ASP cc_start: 0.9020 (p0) cc_final: 0.8586 (p0) REVERT: H 75 LYS cc_start: 0.9449 (mtmt) cc_final: 0.9158 (mtmt) REVERT: H 78 LEU cc_start: 0.9429 (tp) cc_final: 0.9164 (tp) REVERT: H 91 PHE cc_start: 0.9114 (m-80) cc_final: 0.8817 (m-80) REVERT: H 100 ASP cc_start: 0.9261 (t0) cc_final: 0.8922 (t0) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2615 time to fit residues: 65.7856 Evaluate side-chains 106 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17156 Z= 0.222 Angle : 0.622 9.426 23296 Z= 0.316 Chirality : 0.046 0.375 2913 Planarity : 0.006 0.198 2833 Dihedral : 7.532 57.789 4264 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1918 helix: -0.46 (0.26), residues: 390 sheet: -0.31 (0.23), residues: 493 loop : -0.94 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 112 HIS 0.006 0.001 HIS E 249 PHE 0.016 0.001 PHE E 383 TYR 0.018 0.002 TYR E 217 ARG 0.018 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8379 (m-10) cc_final: 0.8063 (m-10) REVERT: A 104 MET cc_start: 0.9170 (tmm) cc_final: 0.8909 (tmm) REVERT: A 150 MET cc_start: 0.8485 (ptp) cc_final: 0.8107 (ptt) REVERT: A 425 ASN cc_start: 0.8117 (p0) cc_final: 0.7613 (p0) REVERT: A 494 LEU cc_start: 0.8909 (mt) cc_final: 0.8373 (mt) REVERT: B 528 SER cc_start: 0.9338 (m) cc_final: 0.8747 (p) REVERT: B 626 MET cc_start: 0.8502 (mmp) cc_final: 0.8137 (mmm) REVERT: B 647 GLU cc_start: 0.9230 (pp20) cc_final: 0.8890 (pp20) REVERT: B 651 ASN cc_start: 0.9262 (p0) cc_final: 0.8780 (p0) REVERT: B 657 GLU cc_start: 0.9198 (mp0) cc_final: 0.8784 (mp0) REVERT: C 150 MET cc_start: 0.9326 (mmp) cc_final: 0.9033 (mmp) REVERT: C 186 ARG cc_start: 0.7733 (mmp80) cc_final: 0.7097 (ptm160) REVERT: C 217 TYR cc_start: 0.7268 (m-10) cc_final: 0.6989 (m-10) REVERT: C 381 GLU cc_start: 0.9036 (tp30) cc_final: 0.8543 (tp30) REVERT: C 426 MET cc_start: 0.6049 (tpp) cc_final: 0.5648 (tpp) REVERT: C 434 MET cc_start: 0.8161 (ppp) cc_final: 0.7888 (ppp) REVERT: C 475 MET cc_start: 0.8478 (mmm) cc_final: 0.8275 (mmm) REVERT: D 584 GLU cc_start: 0.9373 (tp30) cc_final: 0.9165 (tp30) REVERT: E 69 TRP cc_start: 0.8246 (m-90) cc_final: 0.7778 (m-90) REVERT: E 103 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8322 (tp-100) REVERT: E 107 ASP cc_start: 0.8721 (m-30) cc_final: 0.8072 (m-30) REVERT: E 150 MET cc_start: 0.9110 (mmp) cc_final: 0.8846 (mmm) REVERT: E 434 MET cc_start: 0.9042 (mtm) cc_final: 0.8748 (mtm) REVERT: F 530 MET cc_start: 0.9348 (mtp) cc_final: 0.8976 (mtt) REVERT: F 535 MET cc_start: 0.8658 (mmp) cc_final: 0.8318 (tmm) REVERT: F 545 LEU cc_start: 0.9256 (tp) cc_final: 0.8996 (tp) REVERT: F 574 LYS cc_start: 0.8697 (tttp) cc_final: 0.8466 (tttm) REVERT: F 626 MET cc_start: 0.8235 (tpp) cc_final: 0.7923 (tpp) REVERT: F 633 LYS cc_start: 0.9710 (mttt) cc_final: 0.9357 (mmmt) REVERT: F 655 LYS cc_start: 0.9575 (ttmm) cc_final: 0.9051 (ttmm) REVERT: H 53 ASP cc_start: 0.8973 (p0) cc_final: 0.8517 (p0) REVERT: H 75 LYS cc_start: 0.9452 (mtmt) cc_final: 0.9129 (mtmt) REVERT: H 78 LEU cc_start: 0.9382 (tp) cc_final: 0.9162 (tp) REVERT: H 91 PHE cc_start: 0.9094 (m-80) cc_final: 0.8769 (m-80) REVERT: H 100 ASP cc_start: 0.9205 (t0) cc_final: 0.8874 (t0) REVERT: L 88 CYS cc_start: 0.7050 (t) cc_final: 0.6738 (t) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2546 time to fit residues: 63.2619 Evaluate side-chains 115 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17156 Z= 0.198 Angle : 0.597 9.435 23296 Z= 0.304 Chirality : 0.045 0.261 2913 Planarity : 0.005 0.179 2833 Dihedral : 7.262 57.386 4264 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1918 helix: -0.52 (0.25), residues: 400 sheet: -0.28 (0.23), residues: 494 loop : -0.92 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 610 HIS 0.006 0.001 HIS E 249 PHE 0.014 0.001 PHE E 383 TYR 0.019 0.001 TYR E 217 ARG 0.016 0.000 ARG E 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8360 (m-10) cc_final: 0.8064 (m-10) REVERT: A 150 MET cc_start: 0.8524 (ptp) cc_final: 0.8131 (ptt) REVERT: A 425 ASN cc_start: 0.8051 (p0) cc_final: 0.7592 (p0) REVERT: A 494 LEU cc_start: 0.8923 (mt) cc_final: 0.8679 (mt) REVERT: B 528 SER cc_start: 0.9356 (m) cc_final: 0.8915 (p) REVERT: B 626 MET cc_start: 0.8475 (mmp) cc_final: 0.8048 (mmm) REVERT: B 647 GLU cc_start: 0.9260 (pp20) cc_final: 0.8910 (pp20) REVERT: B 651 ASN cc_start: 0.9254 (p0) cc_final: 0.8716 (p0) REVERT: B 657 GLU cc_start: 0.9157 (mp0) cc_final: 0.8694 (mp0) REVERT: C 150 MET cc_start: 0.9330 (mmp) cc_final: 0.9044 (mmp) REVERT: C 217 TYR cc_start: 0.7023 (m-10) cc_final: 0.6712 (m-10) REVERT: C 381 GLU cc_start: 0.9016 (tp30) cc_final: 0.8481 (tp30) REVERT: C 434 MET cc_start: 0.8103 (ppp) cc_final: 0.7834 (ppp) REVERT: C 475 MET cc_start: 0.8428 (mmm) cc_final: 0.8164 (mmm) REVERT: D 610 TRP cc_start: 0.7134 (p90) cc_final: 0.6541 (p90) REVERT: E 69 TRP cc_start: 0.8209 (m-90) cc_final: 0.7709 (m-10) REVERT: E 103 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8429 (tp-100) REVERT: E 107 ASP cc_start: 0.8695 (m-30) cc_final: 0.8027 (m-30) REVERT: E 150 MET cc_start: 0.9053 (mmp) cc_final: 0.8814 (mmm) REVERT: E 279 ASN cc_start: 0.9052 (t0) cc_final: 0.8455 (t0) REVERT: E 434 MET cc_start: 0.9049 (mtm) cc_final: 0.8710 (mtm) REVERT: F 530 MET cc_start: 0.9342 (mtp) cc_final: 0.8970 (mtt) REVERT: F 535 MET cc_start: 0.8712 (mmp) cc_final: 0.8345 (tmm) REVERT: F 536 THR cc_start: 0.8779 (p) cc_final: 0.8498 (p) REVERT: F 545 LEU cc_start: 0.9211 (tp) cc_final: 0.8999 (tp) REVERT: F 626 MET cc_start: 0.8174 (tpp) cc_final: 0.7767 (tpp) REVERT: F 633 LYS cc_start: 0.9704 (mttt) cc_final: 0.9352 (mmmt) REVERT: F 655 LYS cc_start: 0.9584 (ttmm) cc_final: 0.9079 (ttmm) REVERT: F 660 LEU cc_start: 0.8156 (mm) cc_final: 0.7894 (pp) REVERT: H 53 ASP cc_start: 0.8953 (p0) cc_final: 0.8502 (p0) REVERT: H 75 LYS cc_start: 0.9454 (mtmt) cc_final: 0.9101 (mtmt) REVERT: H 78 LEU cc_start: 0.9457 (tp) cc_final: 0.9240 (tp) REVERT: H 91 PHE cc_start: 0.9098 (m-80) cc_final: 0.8761 (m-80) REVERT: H 100 ASP cc_start: 0.9202 (t0) cc_final: 0.8874 (t0) REVERT: L 42 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8736 (mmmt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2520 time to fit residues: 64.1208 Evaluate side-chains 116 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 28 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.037635 restraints weight = 98411.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.039213 restraints weight = 58465.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.040340 restraints weight = 40713.618| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17156 Z= 0.228 Angle : 0.618 9.439 23296 Z= 0.312 Chirality : 0.045 0.258 2913 Planarity : 0.005 0.168 2833 Dihedral : 7.299 57.995 4264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1918 helix: -0.47 (0.26), residues: 399 sheet: -0.30 (0.23), residues: 492 loop : -0.95 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.005 0.001 HIS E 249 PHE 0.017 0.002 PHE L 98 TYR 0.017 0.002 TYR C 484 ARG 0.015 0.000 ARG E 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.73 seconds wall clock time: 52 minutes 44.39 seconds (3164.39 seconds total)