Starting phenix.real_space_refine on Fri Nov 17 18:07:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/11_2023/6ulc_20813_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/11_2023/6ulc_20813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/11_2023/6ulc_20813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/11_2023/6ulc_20813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/11_2023/6ulc_20813_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/11_2023/6ulc_20813_neut_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12400 2.51 5 N 3272 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 589": "OD1" <-> "OD2" Residue "D GLU 662": "OE1" <-> "OE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 183": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19968 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "F" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "H" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1836 Classifications: {'peptide': 240} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 227} Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1593 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.93, per 1000 atoms: 0.50 Number of scatterers: 19968 At special positions: 0 Unit cell: (139.4, 195.16, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4184 8.00 N 3272 7.00 C 12400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=1.91 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 385 " distance=1.92 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 418 " distance=2.28 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.27 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=1.83 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=1.92 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=1.90 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 385 " distance=1.92 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 418 " distance=2.28 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 385 " distance=2.26 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 418 " distance=1.82 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.05 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=1.92 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.91 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 385 " distance=1.90 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 418 " distance=2.29 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 385 " distance=2.27 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 418 " distance=1.84 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=1.91 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=3, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA a 3 " - " MAN a 7 " " MAN a 4 " - " MAN a 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 6 " BETA1-2 " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG G 5 " - " GAL G 6 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG m 1 " - " FUC m 4 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 608 " - " ASN A 138 " " NAG A 609 " - " ASN A 145 " " NAG A 615 " - " ASN A 188 " " NAG A 621 " - " ASN A 234 " " NAG A 622 " - " ASN A 241 " " NAG A 626 " - " ASN A 276 " " NAG A 627 " - " ASN A 289 " " NAG A 628 " - " ASN A 295 " " NAG A 629 " - " ASN A 301 " " NAG A 630 " - " ASN A 332 " " NAG A 631 " - " ASN A 355 " " NAG A 637 " - " ASN A 394 " " NAG A 638 " - " ASN A 398 " " NAG A 639 " - " ASN A 411 " " NAG A 640 " - " ASN A 448 " " NAG A 641 " - " ASN A 463 " " NAG B 903 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 134 " " NAG C 614 " - " ASN C 197 " " NAG C 615 " - " ASN C 234 " " NAG C 618 " - " ASN C 276 " " NAG C 619 " - " ASN C 289 " " NAG C 620 " - " ASN C 295 " " NAG C 621 " - " ASN C 301 " " NAG C 622 " - " ASN C 332 " " NAG C 623 " - " ASN C 355 " " NAG C 627 " - " ASN C 386 " " NAG C 628 " - " ASN C 394 " " NAG C 629 " - " ASN C 411 " " NAG C 630 " - " ASN C 448 " " NAG D 901 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 619 " - " ASN E 188 " " NAG E 625 " - " ASN E 241 " " NAG E 629 " - " ASN E 276 " " NAG E 630 " - " ASN E 289 " " NAG E 634 " - " ASN E 301 " " NAG E 646 " - " ASN E 394 " " NAG E 653 " - " ASN E 448 " " NAG E 654 " - " ASN E 463 " " NAG F 901 " - " ASN F 611 " " NAG F 902 " - " ASN F 625 " " NAG G 1 " - " ASN A 134 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 363 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN B 611 " " NAG P 1 " - " ASN B 637 " " NAG Q 1 " - " ASN C 138 " " NAG R 1 " - " ASN C 145 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN E 134 " " NAG X 1 " - " ASN E 138 " " NAG Y 1 " - " ASN E 145 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 160 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 234 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 355 " " NAG h 1 " - " ASN E 363 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 398 " " NAG k 1 " - " ASN E 411 " " NAG l 1 " - " ASN F 637 " " NAG m 1 " - " ASN A 156 " " NAG n 1 " - " ASN L 24 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.83 Conformation dependent library (CDL) restraints added in 3.4 seconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 39 sheets defined 17.8% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 58 through 61 No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 100 through 118 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 336 through 348 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 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.568A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 546 through 552 removed outlier: 3.657A pdb=" N GLN B 552 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 629 through 634 removed outlier: 3.846A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 Processing helix chain 'B' and resid 651 through 653 No H-bonds generated for 'chain 'B' and resid 651 through 653' Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.753A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 100 through 117 Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 335 through 348 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 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.862A pdb=" N LYS D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 551 removed outlier: 3.684A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 547 through 551' Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 631 through 634 removed outlier: 3.614A pdb=" N GLU D 634 " --> pdb=" O TRP D 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 631 through 634' Processing helix chain 'D' and resid 639 through 652 removed outlier: 4.338A pdb=" N LYS D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 335 through 348 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 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 477 through 485 removed outlier: 4.776A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS E 485 " --> pdb=" O SER E 481 " (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 543 removed outlier: 4.322A pdb=" N LYS F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 554 removed outlier: 4.217A pdb=" N GLN F 552 " --> pdb=" O VAL F 549 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER F 553 " --> pdb=" O GLN F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 621 through 624 No H-bonds generated for 'chain 'F' and resid 621 through 624' Processing helix chain 'F' and resid 629 through 634 Processing helix chain 'F' and resid 636 through 652 removed outlier: 4.661A pdb=" N HIS F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN F 650 " --> pdb=" O ILE F 646 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) 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 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'L' and resid 122 through 125 No H-bonds generated for 'chain 'L' and resid 122 through 125' Processing helix chain 'L' and resid 182 through 187 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 83 through 86 Processing sheet with id= C, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= D, first strand: chain 'A' and resid 129 through 132 Processing sheet with id= E, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.609A pdb=" N LEU A 452 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LYS A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 294 through 297 Processing sheet with id= H, first strand: chain 'A' and resid 304 through 308 Processing sheet with id= I, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.850A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= K, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'C' and resid 84 through 86 Processing sheet with id= M, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= N, first strand: chain 'C' and resid 154 through 162 Processing sheet with id= O, first strand: chain 'C' and resid 271 through 273 Processing sheet with id= P, first strand: chain 'C' and resid 294 through 297 Processing sheet with id= Q, first strand: chain 'C' and resid 305 through 308 Processing sheet with id= R, first strand: chain 'C' and resid 374 through 378 Processing sheet with id= S, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= T, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'E' and resid 91 through 93 Processing sheet with id= V, first strand: chain 'E' and resid 129 through 132 Processing sheet with id= W, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= X, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= Y, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.423A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LYS E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 414 through 417 removed outlier: 3.761A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 305 through 308 Processing sheet with id= AB, first strand: chain 'E' and resid 374 through 378 Processing sheet with id= AC, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AD, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.240A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 100 through 100B Processing sheet with id= AF, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.839A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 150 through 154 Processing sheet with id= AH, first strand: chain 'H' and resid 127 through 130 removed outlier: 7.522A pdb=" N THR H 135 " --> pdb=" O LYS H 129 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 9 through 13 removed outlier: 5.614A pdb=" N LYS L 103 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'L' and resid 19 through 23 Processing sheet with id= AK, first strand: chain 'L' and resid 85 through 90 removed outlier: 5.180A pdb=" N GLN L 37 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 116 through 118 removed outlier: 6.006A pdb=" N TYR L 172 " --> pdb=" O ASP L 138 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 145 through 150 516 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 11.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6266 1.36 - 1.50: 5752 1.50 - 1.64: 8172 1.64 - 1.78: 3 1.78 - 1.93: 151 Bond restraints: 20344 Sorted by residual: bond pdb=" C2 MAN G 4 " pdb=" O2 MAN G 4 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.926 -0.118 3.30e-02 9.18e+02 1.29e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.923 -0.115 3.30e-02 9.18e+02 1.22e+01 bond pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 1.808 1.919 -0.111 3.30e-02 9.18e+02 1.13e+01 ... (remaining 20339 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.87: 665 106.87 - 113.69: 12126 113.69 - 120.51: 6907 120.51 - 127.33: 7684 127.33 - 134.15: 270 Bond angle restraints: 27652 Sorted by residual: angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C GLU D 560 " pdb=" N ALA D 561 " pdb=" CA ALA D 561 " ideal model delta sigma weight residual 121.81 114.19 7.62 1.83e+00 2.99e-01 1.73e+01 angle pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta sigma weight residual 125.02 132.01 -6.99 1.76e+00 3.23e-01 1.58e+01 angle pdb=" C GLU F 560 " pdb=" N ALA F 561 " pdb=" CA ALA F 561 " ideal model delta sigma weight residual 120.88 114.91 5.97 1.62e+00 3.81e-01 1.36e+01 angle pdb=" C VAL E 68 " pdb=" N TRP E 69 " pdb=" CA TRP E 69 " ideal model delta sigma weight residual 125.02 131.17 -6.15 1.76e+00 3.23e-01 1.22e+01 ... (remaining 27647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 9882 17.36 - 34.71: 1019 34.71 - 52.07: 193 52.07 - 69.42: 52 69.42 - 86.78: 20 Dihedral angle restraints: 11166 sinusoidal: 4508 harmonic: 6658 Sorted by residual: dihedral pdb=" CA GLU L 198 " pdb=" C GLU L 198 " pdb=" N GLY L 199 " pdb=" CA GLY L 199 " ideal model delta harmonic sigma weight residual -180.00 -128.94 -51.06 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA GLY E 187 " pdb=" C GLY E 187 " pdb=" N ASN E 188 " pdb=" CA ASN E 188 " ideal model delta harmonic sigma weight residual 180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 176.09 -83.09 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 11163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3407 0.140 - 0.280: 108 0.280 - 0.420: 19 0.420 - 0.560: 3 0.560 - 0.700: 1 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.14e+02 chirality pdb=" C1 MAN a 4 " pdb=" O6 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3535 not shown) Planarity restraints: 3417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 409 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO E 410 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 410 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 410 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 114 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" CD GLN C 114 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN C 114 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN C 114 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 201 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO H 202 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " 0.033 5.00e-02 4.00e+02 ... (remaining 3414 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 524 2.65 - 3.21: 19852 3.21 - 3.77: 30438 3.77 - 4.34: 41139 4.34 - 4.90: 65424 Nonbonded interactions: 157377 Sorted by model distance: nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.086 2.440 nonbonded pdb=" OG SER A 132 " pdb=" OD1 ASN A 156 " model vdw 2.086 2.440 nonbonded pdb=" O ILE F 635 " pdb=" OG1 THR F 639 " model vdw 2.088 2.440 nonbonded pdb=" OG1 THR L 18 " pdb=" O ILE L 75 " model vdw 2.088 2.440 nonbonded pdb=" O ILE B 635 " pdb=" OG1 THR B 639 " model vdw 2.090 2.440 ... (remaining 157372 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' and (resid 32 through 507 or resid 601 through 628)) selection = (chain 'C' and (resid 32 through 507 or resid 601 through 622)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 521 through 664 or resid 901)) } ncs_group { reference = (chain 'G' and (resid 1 or resid 4)) selection = (chain 'a' and (resid 2 or resid 5)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'h' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.850 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 55.820 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.220 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 20344 Z= 0.380 Angle : 0.939 9.746 27652 Z= 0.437 Chirality : 0.068 0.700 3538 Planarity : 0.004 0.067 3341 Dihedral : 14.544 86.778 6738 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.29 % Allowed : 2.26 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.14), residues: 2285 helix: -2.64 (0.20), residues: 370 sheet: -2.93 (0.18), residues: 517 loop : -3.21 (0.14), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 284 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 289 average time/residue: 0.3543 time to fit residues: 152.1987 Evaluate side-chains 154 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 2.186 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1694 time to fit residues: 4.1379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 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 478 ASN B 563 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 440 GLN C 461 ASN E 82 GLN E 183 GLN E 186 ASN E 287 GLN E 343 HIS E 344 GLN E 377 ASN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 20344 Z= 0.347 Angle : 0.919 30.648 27652 Z= 0.424 Chirality : 0.060 0.587 3538 Planarity : 0.005 0.051 3341 Dihedral : 5.957 34.625 2466 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.38 % Favored : 88.49 % Rotamer: Outliers : 0.69 % Allowed : 8.49 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.15), residues: 2285 helix: -1.91 (0.22), residues: 369 sheet: -2.37 (0.20), residues: 473 loop : -2.85 (0.15), residues: 1443 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 2.265 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 outliers start: 14 outliers final: 4 residues processed: 202 average time/residue: 0.3623 time to fit residues: 110.4353 Evaluate side-chains 128 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1846 time to fit residues: 4.3548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 183 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 20344 Z= 0.239 Angle : 0.792 26.157 27652 Z= 0.365 Chirality : 0.055 0.446 3538 Planarity : 0.004 0.051 3341 Dihedral : 5.898 37.287 2466 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.93 % Favored : 91.03 % Rotamer: Outliers : 0.15 % Allowed : 4.96 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.16), residues: 2285 helix: -1.43 (0.24), residues: 371 sheet: -1.76 (0.22), residues: 465 loop : -2.65 (0.15), residues: 1449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 2.186 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 outliers start: 3 outliers final: 1 residues processed: 193 average time/residue: 0.3537 time to fit residues: 103.1278 Evaluate side-chains 122 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.250 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2041 time to fit residues: 3.1403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.0370 chunk 139 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 20344 Z= 0.383 Angle : 0.906 26.258 27652 Z= 0.423 Chirality : 0.057 0.515 3538 Planarity : 0.005 0.048 3341 Dihedral : 6.280 36.885 2466 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.60 % Favored : 87.35 % Rotamer: Outliers : 0.15 % Allowed : 5.20 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.16), residues: 2285 helix: -1.63 (0.24), residues: 365 sheet: -1.78 (0.22), residues: 453 loop : -2.63 (0.15), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 2.193 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 outliers start: 3 outliers final: 1 residues processed: 159 average time/residue: 0.3542 time to fit residues: 86.3984 Evaluate side-chains 108 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 2.421 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1889 time to fit residues: 3.4342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 20344 Z= 0.350 Angle : 0.881 22.075 27652 Z= 0.412 Chirality : 0.056 0.498 3538 Planarity : 0.005 0.048 3341 Dihedral : 6.388 37.279 2466 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.08 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.16), residues: 2285 helix: -1.42 (0.25), residues: 348 sheet: -1.75 (0.22), residues: 461 loop : -2.52 (0.15), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.287 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 outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3542 time to fit residues: 85.7774 Evaluate side-chains 113 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.0670 chunk 220 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 0.0070 chunk 115 optimal weight: 7.9990 overall best weight: 1.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 577 GLN E 183 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN F 590 GLN F 607 ASN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 20344 Z= 0.240 Angle : 0.816 24.488 27652 Z= 0.375 Chirality : 0.055 0.480 3538 Planarity : 0.004 0.046 3341 Dihedral : 6.084 34.918 2466 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.55 % Favored : 88.40 % Rotamer: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.16), residues: 2285 helix: -1.30 (0.24), residues: 375 sheet: -1.51 (0.22), residues: 472 loop : -2.46 (0.15), residues: 1438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 2.424 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 outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.3589 time to fit residues: 95.0496 Evaluate side-chains 117 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 20344 Z= 0.476 Angle : 1.065 22.573 27652 Z= 0.501 Chirality : 0.062 0.543 3538 Planarity : 0.006 0.090 3341 Dihedral : 6.985 37.191 2466 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.27 % Favored : 85.60 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.16), residues: 2285 helix: -1.97 (0.23), residues: 364 sheet: -1.47 (0.23), residues: 442 loop : -2.63 (0.15), residues: 1479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.012 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 outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3773 time to fit residues: 82.5723 Evaluate side-chains 108 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 overall best weight: 3.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188AASN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 591 GLN D 607 ASN E 183 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 20344 Z= 0.310 Angle : 0.912 22.226 27652 Z= 0.422 Chirality : 0.058 0.597 3538 Planarity : 0.005 0.067 3341 Dihedral : 6.679 34.775 2466 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.87 % Favored : 87.09 % Rotamer: Outliers : 0.10 % Allowed : 1.77 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.16), residues: 2285 helix: -1.71 (0.24), residues: 356 sheet: -1.61 (0.22), residues: 495 loop : -2.50 (0.15), residues: 1434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 2.443 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 outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.3656 time to fit residues: 86.4329 Evaluate side-chains 110 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 183 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 20344 Z= 0.282 Angle : 0.891 27.074 27652 Z= 0.409 Chirality : 0.057 0.487 3538 Planarity : 0.005 0.060 3341 Dihedral : 6.461 33.979 2466 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.04 % Favored : 86.91 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.16), residues: 2285 helix: -1.67 (0.24), residues: 361 sheet: -1.70 (0.22), residues: 482 loop : -2.44 (0.16), residues: 1442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.489 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 outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.4065 time to fit residues: 94.5477 Evaluate side-chains 113 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2297 time to fit residues: 3.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 132 optimal weight: 0.0980 chunk 102 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 650 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 577 GLN E 114 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20344 Z= 0.230 Angle : 0.849 26.879 27652 Z= 0.387 Chirality : 0.056 0.462 3538 Planarity : 0.004 0.046 3341 Dihedral : 6.183 33.208 2466 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.12 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.16), residues: 2285 helix: -1.33 (0.25), residues: 356 sheet: -1.58 (0.22), residues: 503 loop : -2.35 (0.16), residues: 1426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.229 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 outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3526 time to fit residues: 94.7641 Evaluate side-chains 123 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.077082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.065025 restraints weight = 143720.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.066333 restraints weight = 98915.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.067261 restraints weight = 75145.225| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20344 Z= 0.240 Angle : 0.847 26.494 27652 Z= 0.388 Chirality : 0.055 0.461 3538 Planarity : 0.004 0.048 3341 Dihedral : 6.049 32.343 2466 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.90 % Favored : 88.05 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), residues: 2285 helix: -1.22 (0.25), residues: 371 sheet: -1.45 (0.23), residues: 485 loop : -2.30 (0.16), residues: 1429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.34 seconds wall clock time: 62 minutes 43.91 seconds (3763.91 seconds total)