Starting phenix.real_space_refine on Tue Dec 12 03:21:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/12_2023/6ulc_20813_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/12_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_20813/12_2023/6ulc_20813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/12_2023/6ulc_20813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/12_2023/6ulc_20813_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ulc_20813/12_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19968 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3717 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "F" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1167 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain: "H" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1836 Classifications: {'peptide': 240} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 227} Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1593 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 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 dihedrals: 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 dihedrals: 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 dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 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 dihedrals: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 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 dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.56, per 1000 atoms: 0.53 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: 10.10 Conformation dependent library (CDL) restraints added in 3.2 seconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... 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: 3.75 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: 6.11 Time building geometry restraints manager: 10.69 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 - 24.22: 12426 24.22 - 48.43: 803 48.43 - 72.65: 159 72.65 - 96.86: 46 96.86 - 121.08: 21 Dihedral angle restraints: 13455 sinusoidal: 6797 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 13452 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: 0.400 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: 2.700 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 55.320 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.430 ------------------------------------------------------------------------------- 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 : 16.705 121.075 9027 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.29 % Allowed : 2.26 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.14), residues: 2285 helix: -2.64 (0.20), residues: 370 sheet: -2.93 (0.18), residues: 517 loop : -3.21 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.012 0.001 HIS E 105 PHE 0.013 0.001 PHE L 49 TYR 0.012 0.001 TYR B 643 ARG 0.003 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 284 time to evaluate : 2.279 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: 0.3511 time to fit residues: 151.5230 Evaluate side-chains 154 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 2.212 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1726 time to fit residues: 4.2068 ------------------------------------------------------------------------------- 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 344 GLN E 377 ASN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 20344 Z= 0.343 Angle : 0.914 28.206 27652 Z= 0.423 Chirality : 0.060 0.578 3538 Planarity : 0.005 0.053 3341 Dihedral : 13.071 113.379 4755 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.38 % Favored : 88.53 % Rotamer: Outliers : 0.69 % Allowed : 8.54 % Favored : 90.77 % 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: -3.78 (0.15), residues: 2285 helix: -1.93 (0.22), residues: 369 sheet: -2.38 (0.20), residues: 471 loop : -2.86 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 395 HIS 0.016 0.002 HIS A 105 PHE 0.024 0.003 PHE E 382 TYR 0.019 0.002 TYR F 643 ARG 0.006 0.001 ARG A 192 *********************** 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 : 2.107 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 outliers start: 14 outliers final: 4 residues processed: 202 average time/residue: 0.3558 time to fit residues: 108.3472 Evaluate side-chains 128 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1954 time to fit residues: 4.5609 ------------------------------------------------------------------------------- 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: 5.9990 chunk 140 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 184 optimal weight: 0.0870 chunk 205 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 72 HIS E 103 GLN E 183 GLN E 343 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20344 Z= 0.237 Angle : 0.795 25.182 27652 Z= 0.367 Chirality : 0.055 0.483 3538 Planarity : 0.004 0.055 3341 Dihedral : 11.872 113.437 4755 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.84 % Favored : 91.12 % Rotamer: Outliers : 0.15 % Allowed : 5.25 % Favored : 94.60 % 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: -1.44 (0.24), residues: 371 sheet: -1.75 (0.22), residues: 467 loop : -2.65 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 395 HIS 0.011 0.001 HIS A 105 PHE 0.018 0.002 PHE E 382 TYR 0.045 0.002 TYR B 643 ARG 0.006 0.000 ARG B 579 *********************** 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 196 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 2.122 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: 3 outliers final: 1 residues processed: 194 average time/residue: 0.3559 time to fit residues: 104.7644 Evaluate side-chains 117 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1801 time to fit residues: 3.1892 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 197 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 overall best weight: 6.0186 ------------------------------------------------------------------------------- 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** C 478 ASN 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 20344 Z= 0.439 Angle : 0.968 25.286 27652 Z= 0.455 Chirality : 0.059 0.557 3538 Planarity : 0.006 0.051 3341 Dihedral : 12.025 113.784 4755 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.87 % Favored : 87.09 % Rotamer: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -3.37 (0.16), residues: 2285 helix: -1.75 (0.23), residues: 374 sheet: -1.76 (0.22), residues: 460 loop : -2.68 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 395 HIS 0.013 0.002 HIS A 105 PHE 0.023 0.003 PHE A 210 TYR 0.028 0.003 TYR F 643 ARG 0.009 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 2.117 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: 2 outliers final: 1 residues processed: 153 average time/residue: 0.3552 time to fit residues: 83.4820 Evaluate side-chains 107 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.168 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1730 time to fit residues: 3.1908 ------------------------------------------------------------------------------- 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: 0.9980 chunk 125 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 chunk 164 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- 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 E 183 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN F 590 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 20344 Z= 0.281 Angle : 0.831 20.617 27652 Z= 0.386 Chirality : 0.055 0.515 3538 Planarity : 0.005 0.049 3341 Dihedral : 11.431 112.579 4755 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.07 % Favored : 88.88 % Rotamer: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % 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: -3.11 (0.16), residues: 2285 helix: -1.30 (0.25), residues: 356 sheet: -1.69 (0.22), residues: 478 loop : -2.52 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 112 HIS 0.012 0.001 HIS A 105 PHE 0.019 0.002 PHE E 382 TYR 0.029 0.002 TYR D 586 ARG 0.014 0.001 ARG H 94 *********************** 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 161 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.067 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: 1 outliers final: 0 residues processed: 160 average time/residue: 0.3524 time to fit residues: 85.5671 Evaluate side-chains 111 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9809 ------------------------------------------------------------------------------- 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: 0.8980 chunk 198 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 220 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ** 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 607 ASN ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20344 Z= 0.241 Angle : 0.810 24.559 27652 Z= 0.372 Chirality : 0.055 0.496 3538 Planarity : 0.004 0.047 3341 Dihedral : 10.852 111.626 4755 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.29 % Favored : 88.67 % Rotamer: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % 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: -1.18 (0.25), residues: 358 sheet: -1.52 (0.22), residues: 510 loop : -2.44 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 571 HIS 0.011 0.001 HIS E 105 PHE 0.014 0.002 PHE E 382 TYR 0.048 0.002 TYR B 643 ARG 0.008 0.001 ARG B 620 *********************** 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 169 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.958 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: 1 residues processed: 169 average time/residue: 0.3488 time to fit residues: 89.3550 Evaluate side-chains 117 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2297 time to fit residues: 3.5068 ------------------------------------------------------------------------------- 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: 0.2980 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 0.0980 chunk 123 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100PASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20344 Z= 0.268 Angle : 0.830 24.489 27652 Z= 0.384 Chirality : 0.055 0.492 3538 Planarity : 0.004 0.045 3341 Dihedral : 10.669 111.047 4755 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.42 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -2.90 (0.16), residues: 2285 helix: -1.27 (0.25), residues: 366 sheet: -1.53 (0.22), residues: 512 loop : -2.36 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 628 HIS 0.010 0.001 HIS A 105 PHE 0.013 0.002 PHE A 210 TYR 0.051 0.002 TYR F 643 ARG 0.007 0.001 ARG B 585 *********************** 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 170 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.022 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 outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3673 time to fit residues: 95.1715 Evaluate side-chains 115 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN C 422 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4549 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= 0.286 Angle : 0.851 23.715 27652 Z= 0.394 Chirality : 0.056 0.517 3538 Planarity : 0.004 0.045 3341 Dihedral : 10.684 110.836 4755 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.08 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % 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: -2.85 (0.16), residues: 2285 helix: -1.18 (0.25), residues: 357 sheet: -1.41 (0.22), residues: 494 loop : -2.37 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 395 HIS 0.009 0.001 HIS E 105 PHE 0.014 0.002 PHE A 317 TYR 0.041 0.002 TYR B 643 ARG 0.011 0.001 ARG E 503 *********************** 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 157 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.007 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: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3474 time to fit residues: 84.0208 Evaluate side-chains 109 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9325 ------------------------------------------------------------------------------- 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: 40.0000 chunk 210 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 337 GLN ** A 432 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20344 Z= 0.289 Angle : 0.863 27.575 27652 Z= 0.398 Chirality : 0.056 0.482 3538 Planarity : 0.004 0.045 3341 Dihedral : 10.655 110.639 4755 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.65 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), residues: 2285 helix: -1.21 (0.25), residues: 339 sheet: -1.53 (0.22), residues: 508 loop : -2.26 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 112 HIS 0.014 0.002 HIS E 105 PHE 0.012 0.002 PHE L 62 TYR 0.019 0.002 TYR A 484 ARG 0.006 0.001 ARG L 61 *********************** 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 157 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.167 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: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3502 time to fit residues: 84.1569 Evaluate side-chains 115 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9145 ------------------------------------------------------------------------------- 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: 20.0000 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 20344 Z= 0.328 Angle : 0.903 26.856 27652 Z= 0.418 Chirality : 0.057 0.480 3538 Planarity : 0.005 0.050 3341 Dihedral : 10.949 111.364 4755 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.65 % Favored : 86.30 % Rotamer: Outliers : 0.05 % Allowed : 0.54 % Favored : 99.41 % 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: -2.97 (0.16), residues: 2285 helix: -1.42 (0.24), residues: 348 sheet: -1.60 (0.22), residues: 505 loop : -2.35 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 112 HIS 0.020 0.002 HIS E 105 PHE 0.016 0.002 PHE A 210 TYR 0.020 0.002 TYR F 643 ARG 0.009 0.001 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 2.252 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: 1 outliers final: 0 residues processed: 149 average time/residue: 0.3477 time to fit residues: 80.0029 Evaluate side-chains 117 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9698 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 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 A 466 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.075870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063879 restraints weight = 143854.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.065184 restraints weight = 98631.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.066107 restraints weight = 74698.763| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20344 Z= 0.271 Angle : 0.851 26.747 27652 Z= 0.393 Chirality : 0.056 0.467 3538 Planarity : 0.004 0.045 3341 Dihedral : 10.666 111.531 4755 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.43 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.17), residues: 2285 helix: -1.27 (0.25), residues: 343 sheet: -1.59 (0.21), residues: 522 loop : -2.32 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 596 HIS 0.019 0.001 HIS E 105 PHE 0.012 0.002 PHE E 382 TYR 0.037 0.002 TYR B 643 ARG 0.007 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.46 seconds wall clock time: 62 minutes 40.62 seconds (3760.62 seconds total)