Starting phenix.real_space_refine on Mon Feb 19 22:55:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoz_11331/02_2024/6zoz_11331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoz_11331/02_2024/6zoz_11331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoz_11331/02_2024/6zoz_11331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoz_11331/02_2024/6zoz_11331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoz_11331/02_2024/6zoz_11331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoz_11331/02_2024/6zoz_11331_updated.pdb" } resolution = 3.5 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= 0.005 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 123 5.16 5 C 16556 2.51 5 N 4240 2.21 5 O 5092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A ARG 843": "NH1" <-> "NH2" Residue "A PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 990": "OD1" <-> "OD2" Residue "A ASP 1037": "OD1" <-> "OD2" Residue "A TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 721": "OE1" <-> "OE2" Residue "B GLU 744": "OE1" <-> "OE2" Residue "B GLU 769": "OE1" <-> "OE2" Residue "B ASP 771": "OD1" <-> "OD2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B ARG 843": "NH1" <-> "NH2" Residue "B PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 990": "OD1" <-> "OD2" Residue "B ASP 1037": "OD1" <-> "OD2" Residue "B TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 721": "OE1" <-> "OE2" Residue "C GLU 744": "OE1" <-> "OE2" Residue "C GLU 769": "OE1" <-> "OE2" Residue "C ASP 771": "OD1" <-> "OD2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C ARG 843": "NH1" <-> "NH2" Residue "C PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 990": "OD1" <-> "OD2" Residue "C ASP 1037": "OD1" <-> "OD2" Residue "C TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26011 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8332 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "B" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8332 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8336 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 13.47, per 1000 atoms: 0.52 Number of scatterers: 26011 At special positions: 0 Unit cell: (126.259, 138.991, 164.455, 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 123 16.00 O 5092 8.00 N 4240 7.00 C 16556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 981 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS C 383 " distance=2.06 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.02 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 981 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.02 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.02 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.02 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 705 " " NAG A1308 " - " ASN A1070 " " NAG A1309 " - " ASN A1094 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 705 " " NAG B1308 " - " ASN B1070 " " NAG B1309 " - " ASN B1094 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 705 " " NAG C1308 " - " ASN C1070 " " NAG C1309 " - " ASN C1094 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 713 " " NAG F 1 " - " ASN A 797 " " NAG G 1 " - " ASN A1130 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 713 " " NAG J 1 " - " ASN B 797 " " NAG K 1 " - " ASN B1130 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 713 " " NAG N 1 " - " ASN C 797 " " NAG O 1 " - " ASN C1130 " Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 4.9 seconds 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 42 sheets defined 23.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.19 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 637 removed outlier: 4.189A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.892A pdb=" N GLN A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 778 Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.545A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 880 Processing helix chain 'A' and resid 894 through 904 Processing helix chain 'A' and resid 909 through 934 removed outlier: 3.583A pdb=" N GLN A 916 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 934 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 963 removed outlier: 4.894A pdb=" N LYS A 943 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP A 946 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1028 removed outlier: 5.301A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 637 removed outlier: 4.189A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 738 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.892A pdb=" N GLN B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 778 Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 845 through 852 removed outlier: 3.545A pdb=" N ASN B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 880 Processing helix chain 'B' and resid 894 through 904 Processing helix chain 'B' and resid 909 through 934 removed outlier: 3.582A pdb=" N GLN B 916 " --> pdb=" O TYR B 913 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS B 917 " --> pdb=" O GLU B 914 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 934 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 963 removed outlier: 4.894A pdb=" N LYS B 943 " --> pdb=" O ALA B 940 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B 946 " --> pdb=" O LYS B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1028 removed outlier: 5.302A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 384 through 387 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 637 removed outlier: 4.189A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 738 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.892A pdb=" N GLN C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 778 Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 845 through 852 removed outlier: 3.545A pdb=" N ASN C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 880 Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 909 through 934 removed outlier: 3.583A pdb=" N GLN C 916 " --> pdb=" O TYR C 913 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS C 917 " --> pdb=" O GLU C 914 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 934 " --> pdb=" O GLN C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 963 removed outlier: 4.895A pdb=" N LYS C 943 " --> pdb=" O ALA C 940 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP C 946 " --> pdb=" O LYS C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1028 removed outlier: 5.302A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 7.792A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 169 through 171 removed outlier: 5.610A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.797A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 325 through 328 removed outlier: 8.529A pdb=" N ILE A 326 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.263A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU A 516 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 687 through 692 removed outlier: 6.188A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 714 through 724 removed outlier: 5.920A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.357A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id= M, first strand: chain 'A' and resid 1090 through 1093 Processing sheet with id= N, first strand: chain 'A' and resid 707 through 713 removed outlier: 6.535A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 27 through 31 removed outlier: 7.792A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.020A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 169 through 171 removed outlier: 5.610A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.798A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 325 through 328 removed outlier: 8.530A pdb=" N ILE B 326 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= V, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= W, first strand: chain 'B' and resid 687 through 692 removed outlier: 6.189A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 714 through 724 removed outlier: 5.919A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.357A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id= AA, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id= AB, first strand: chain 'B' and resid 707 through 713 removed outlier: 6.535A pdb=" N GLN B1067 " --> pdb=" O THR B 712 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 27 through 31 removed outlier: 7.792A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 169 through 171 removed outlier: 5.610A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.797A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 325 through 328 removed outlier: 8.529A pdb=" N ILE C 326 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.263A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU C 516 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 395 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 514 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA C 397 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 512 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 399 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 510 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL C 401 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR C 508 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AJ, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'C' and resid 687 through 692 removed outlier: 6.188A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 714 through 724 removed outlier: 5.920A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.356A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 1076 through 1078 Processing sheet with id= AO, first strand: chain 'C' and resid 1090 through 1093 Processing sheet with id= AP, first strand: chain 'C' and resid 707 through 713 removed outlier: 6.534A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) 933 hydrogen bonds defined for protein. 2241 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: 10.50 Time building geometry restraints manager: 11.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4204 1.31 - 1.44: 7458 1.44 - 1.58: 14778 1.58 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 26590 Sorted by residual: bond pdb=" C4C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C4C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C4C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" NB BLA B1314 " pdb=" C4B BLA B1314 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" NB BLA C1314 " pdb=" C4B BLA C1314 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 26585 not shown) Histogram of bond angle deviations from ideal: 95.73 - 103.39: 218 103.39 - 111.05: 10639 111.05 - 118.71: 10521 118.71 - 126.37: 14499 126.37 - 134.03: 335 Bond angle restraints: 36212 Sorted by residual: angle pdb=" CA GLU C1013 " pdb=" CB GLU C1013 " pdb=" CG GLU C1013 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA GLU B1013 " pdb=" CB GLU B1013 " pdb=" CG GLU B1013 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA GLU A1013 " pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CB LYS A 782 " pdb=" CG LYS A 782 " pdb=" CD LYS A 782 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CB LYS B 782 " pdb=" CG LYS B 782 " pdb=" CD LYS B 782 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 36207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 15358 17.84 - 35.67: 969 35.67 - 53.51: 228 53.51 - 71.34: 87 71.34 - 89.18: 42 Dihedral angle restraints: 16684 sinusoidal: 7344 harmonic: 9340 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.28 -77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.29 -77.71 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.30 -77.70 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 16681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3791 0.080 - 0.161: 472 0.161 - 0.241: 12 0.241 - 0.321: 6 0.321 - 0.402: 6 Chirality restraints: 4287 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4284 not shown) Planarity restraints: 4654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1314 " -0.053 2.00e-02 2.50e+03 6.71e-02 1.12e+02 pdb=" C1A BLA A1314 " 0.152 2.00e-02 2.50e+03 pdb=" C1D BLA A1314 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BLA A1314 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA A1314 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA A1314 " -0.056 2.00e-02 2.50e+03 pdb=" CAD BLA A1314 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA A1314 " -0.101 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " -0.004 2.00e-02 2.50e+03 pdb=" CMD BLA A1314 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1314 " -0.053 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" C1A BLA C1314 " 0.152 2.00e-02 2.50e+03 pdb=" C1D BLA C1314 " -0.015 2.00e-02 2.50e+03 pdb=" C2D BLA C1314 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA C1314 " -0.015 2.00e-02 2.50e+03 pdb=" C4D BLA C1314 " -0.056 2.00e-02 2.50e+03 pdb=" CAD BLA C1314 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1314 " -0.101 2.00e-02 2.50e+03 pdb=" CHD BLA C1314 " -0.003 2.00e-02 2.50e+03 pdb=" CMD BLA C1314 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1314 " -0.053 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" C1A BLA B1314 " 0.152 2.00e-02 2.50e+03 pdb=" C1D BLA B1314 " -0.015 2.00e-02 2.50e+03 pdb=" C2D BLA B1314 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA B1314 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA B1314 " -0.056 2.00e-02 2.50e+03 pdb=" CAD BLA B1314 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA B1314 " -0.101 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " -0.004 2.00e-02 2.50e+03 pdb=" CMD BLA B1314 " 0.069 2.00e-02 2.50e+03 ... (remaining 4651 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 356 2.60 - 3.17: 23835 3.17 - 3.75: 39857 3.75 - 4.32: 56831 4.32 - 4.90: 92703 Nonbonded interactions: 213582 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.025 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.025 2.440 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.025 2.440 nonbonded pdb=" OG SER C 880 " pdb=" O LEU C 890 " model vdw 2.038 2.440 nonbonded pdb=" OG SER A 880 " pdb=" O LEU A 890 " model vdw 2.038 2.440 ... (remaining 213577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 15 through 176 or resid 185 through 1136 or resid 1301 thr \ ough 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.00 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.000 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 71.150 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.007 0.167 26590 Z= 0.498 Angle : 0.782 9.249 36212 Z= 0.401 Chirality : 0.050 0.402 4287 Planarity : 0.005 0.067 4603 Dihedral : 13.204 89.178 10528 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.43 % Allowed : 0.22 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3172 helix: 0.05 (0.18), residues: 783 sheet: -0.03 (0.18), residues: 675 loop : -0.96 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A1044 PHE 0.014 0.001 PHE B 592 TYR 0.011 0.001 TYR C1063 ARG 0.010 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.9238 (mt) cc_final: 0.8929 (mm) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.3327 time to fit residues: 72.9554 Evaluate side-chains 91 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 864 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 5.9990 chunk 241 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 152 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 289 optimal weight: 50.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 783 GLN A 909 GLN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 783 GLN B 909 GLN ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 783 GLN C 909 GLN ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26590 Z= 0.212 Angle : 0.572 7.302 36212 Z= 0.299 Chirality : 0.047 0.347 4287 Planarity : 0.004 0.037 4603 Dihedral : 8.423 99.851 4859 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.50 % Allowed : 4.52 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3172 helix: -0.08 (0.18), residues: 770 sheet: 0.03 (0.18), residues: 698 loop : -0.85 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 64 HIS 0.001 0.001 HIS B1060 PHE 0.012 0.001 PHE A 377 TYR 0.017 0.001 TYR C1134 ARG 0.005 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.3659 time to fit residues: 65.9007 Evaluate side-chains 89 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 313 optimal weight: 0.7980 chunk 258 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN B 99 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 GLN C 99 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26590 Z= 0.168 Angle : 0.514 7.111 36212 Z= 0.272 Chirality : 0.045 0.333 4287 Planarity : 0.004 0.054 4603 Dihedral : 7.189 59.158 4847 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.75 % Allowed : 6.20 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3172 helix: 0.03 (0.18), residues: 785 sheet: 0.22 (0.18), residues: 740 loop : -0.80 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.002 0.000 HIS C1044 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR A1063 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 865 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8982 (mtm) REVERT: C 1013 GLU cc_start: 0.8108 (tp30) cc_final: 0.7804 (tp30) outliers start: 21 outliers final: 8 residues processed: 108 average time/residue: 0.3373 time to fit residues: 64.2614 Evaluate side-chains 89 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 152 optimal weight: 0.0980 chunk 276 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 388 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN B 360 ASN B 388 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 388 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26590 Z= 0.198 Angle : 0.512 7.095 36212 Z= 0.270 Chirality : 0.045 0.329 4287 Planarity : 0.004 0.036 4603 Dihedral : 6.736 57.129 4846 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.90 % Allowed : 7.17 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3172 helix: 0.14 (0.19), residues: 771 sheet: 0.32 (0.18), residues: 737 loop : -0.76 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS C1044 PHE 0.010 0.001 PHE A 377 TYR 0.013 0.001 TYR A1063 ARG 0.004 0.000 ARG B 901 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1013 GLU cc_start: 0.8102 (tp30) cc_final: 0.7849 (tp30) outliers start: 25 outliers final: 16 residues processed: 109 average time/residue: 0.3407 time to fit residues: 64.9195 Evaluate side-chains 94 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 863 ASP Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 229 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26590 Z= 0.315 Angle : 0.573 7.791 36212 Z= 0.299 Chirality : 0.046 0.325 4287 Planarity : 0.004 0.049 4603 Dihedral : 6.536 56.315 4846 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.29 % Allowed : 8.42 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3172 helix: 0.07 (0.19), residues: 755 sheet: 0.26 (0.18), residues: 744 loop : -0.70 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.005 0.001 HIS C1044 PHE 0.012 0.001 PHE C 377 TYR 0.016 0.001 TYR B 833 ARG 0.016 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 34 residues processed: 118 average time/residue: 0.3338 time to fit residues: 69.4223 Evaluate side-chains 115 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 863 ASP Chi-restraints excluded: chain C residue 865 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 308 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26590 Z= 0.216 Angle : 0.514 7.062 36212 Z= 0.271 Chirality : 0.045 0.333 4287 Planarity : 0.004 0.035 4603 Dihedral : 6.296 56.626 4846 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.51 % Allowed : 9.07 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3172 helix: 0.09 (0.19), residues: 762 sheet: 0.41 (0.18), residues: 730 loop : -0.74 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS C1044 PHE 0.009 0.001 PHE C 377 TYR 0.013 0.001 TYR A1063 ARG 0.007 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1030 LEU cc_start: 0.9606 (mt) cc_final: 0.9338 (mp) outliers start: 42 outliers final: 33 residues processed: 129 average time/residue: 0.3264 time to fit residues: 73.6578 Evaluate side-chains 117 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 863 ASP Chi-restraints excluded: chain C residue 865 MET Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 141 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 931 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 GLN C 931 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26590 Z= 0.216 Angle : 0.515 7.023 36212 Z= 0.271 Chirality : 0.045 0.329 4287 Planarity : 0.004 0.040 4603 Dihedral : 6.134 56.165 4846 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.61 % Allowed : 9.50 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3172 helix: 0.12 (0.19), residues: 756 sheet: 0.46 (0.18), residues: 728 loop : -0.71 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS C1044 PHE 0.009 0.001 PHE C 377 TYR 0.012 0.001 TYR A1063 ARG 0.006 0.000 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 96 time to evaluate : 2.976 Fit side-chains revert: symmetry clash REVERT: A 769 GLU cc_start: 0.8336 (tt0) cc_final: 0.8131 (tt0) REVERT: B 984 GLU cc_start: 0.7162 (pm20) cc_final: 0.6944 (pm20) outliers start: 45 outliers final: 36 residues processed: 136 average time/residue: 0.3132 time to fit residues: 74.8796 Evaluate side-chains 124 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 863 ASP Chi-restraints excluded: chain C residue 865 MET Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 897 GLN B 931 GLN C 81 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 GLN C 931 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26590 Z= 0.244 Angle : 0.526 7.037 36212 Z= 0.276 Chirality : 0.045 0.327 4287 Planarity : 0.004 0.039 4603 Dihedral : 5.947 55.997 4842 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.36 % Allowed : 10.14 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3172 helix: 0.04 (0.19), residues: 774 sheet: 0.34 (0.18), residues: 752 loop : -0.71 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS C1044 PHE 0.009 0.001 PHE C 377 TYR 0.012 0.001 TYR A1063 ARG 0.006 0.000 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 3.179 Fit side-chains revert: symmetry clash REVERT: A 769 GLU cc_start: 0.8342 (tt0) cc_final: 0.8136 (tt0) outliers start: 38 outliers final: 36 residues processed: 125 average time/residue: 0.3147 time to fit residues: 70.5687 Evaluate side-chains 123 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 863 ASP Chi-restraints excluded: chain C residue 865 MET Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 4.9990 chunk 294 optimal weight: 0.7980 chunk 268 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 0.0060 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26590 Z= 0.158 Angle : 0.505 9.587 36212 Z= 0.265 Chirality : 0.045 0.330 4287 Planarity : 0.004 0.041 4603 Dihedral : 5.762 56.125 4842 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.18 % Allowed : 10.54 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3172 helix: 0.06 (0.19), residues: 786 sheet: 0.36 (0.18), residues: 712 loop : -0.59 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 64 HIS 0.001 0.000 HIS B1060 PHE 0.009 0.001 PHE C1117 TYR 0.011 0.001 TYR C1063 ARG 0.006 0.000 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 2.774 Fit side-chains revert: symmetry clash REVERT: A 769 GLU cc_start: 0.8317 (tt0) cc_final: 0.8101 (tt0) REVERT: B 984 GLU cc_start: 0.7075 (pm20) cc_final: 0.6761 (pm20) REVERT: B 1030 LEU cc_start: 0.9569 (mt) cc_final: 0.9301 (mp) outliers start: 33 outliers final: 29 residues processed: 135 average time/residue: 0.3068 time to fit residues: 72.3519 Evaluate side-chains 122 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 865 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 5.9990 chunk 302 optimal weight: 0.0970 chunk 184 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 210 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 253 optimal weight: 9.9990 chunk 26 optimal weight: 50.0000 chunk 195 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN B 207 HIS ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 931 GLN C 207 HIS ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 GLN C 931 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26590 Z= 0.263 Angle : 0.537 7.062 36212 Z= 0.281 Chirality : 0.045 0.323 4287 Planarity : 0.004 0.035 4603 Dihedral : 5.756 55.522 4842 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.29 % Allowed : 10.79 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3172 helix: 0.09 (0.19), residues: 779 sheet: 0.33 (0.18), residues: 734 loop : -0.59 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.007 0.001 HIS A 207 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR A1063 ARG 0.006 0.000 ARG A 979 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 3.371 Fit side-chains revert: symmetry clash REVERT: A 769 GLU cc_start: 0.8343 (tt0) cc_final: 0.8130 (tt0) REVERT: B 984 GLU cc_start: 0.7027 (pm20) cc_final: 0.6781 (pm20) outliers start: 36 outliers final: 33 residues processed: 129 average time/residue: 0.3343 time to fit residues: 76.5242 Evaluate side-chains 126 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 865 MET Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 865 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 233 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 GLN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059539 restraints weight = 90531.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061791 restraints weight = 44224.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063247 restraints weight = 28870.072| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26590 Z= 0.210 Angle : 0.519 7.130 36212 Z= 0.273 Chirality : 0.045 0.325 4287 Planarity : 0.004 0.038 4603 Dihedral : 5.733 55.624 4842 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.43 % Allowed : 10.72 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3172 helix: 0.10 (0.19), residues: 779 sheet: 0.36 (0.18), residues: 714 loop : -0.57 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.007 0.001 HIS B 207 PHE 0.009 0.001 PHE C 377 TYR 0.012 0.001 TYR B 421 ARG 0.006 0.000 ARG A 979 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.58 seconds wall clock time: 68 minutes 25.37 seconds (4105.37 seconds total)