Starting phenix.real_space_refine on Tue Feb 20 05:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp2_11334/02_2024/6zp2_11334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp2_11334/02_2024/6zp2_11334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp2_11334/02_2024/6zp2_11334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp2_11334/02_2024/6zp2_11334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp2_11334/02_2024/6zp2_11334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp2_11334/02_2024/6zp2_11334_updated.pdb" } resolution = 3.1 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= 0.007 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 120 5.16 5 C 17106 2.51 5 N 4380 2.21 5 O 5265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "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 GLU 132": "OE1" <-> "OE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "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 GLU 132": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B ASP 848": "OD1" <-> "OD2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "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 GLU 132": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C ASP 848": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8572 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1044} Chain breaks: 4 Chain: "B" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8572 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1044} Chain breaks: 4 Chain: "C" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8572 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1044} Chain breaks: 4 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 265 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} 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: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} 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: 13.80, per 1000 atoms: 0.51 Number of scatterers: 26871 At special positions: 0 Unit cell: (142.174, 151.723, 169.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5265 8.00 N 4380 7.00 C 17106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.99 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 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 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.99 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 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 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.99 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 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 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2102 " - " ASN A 331 " " NAG A2103 " - " ASN A 603 " " NAG A2104 " - " ASN A 616 " " NAG A2105 " - " ASN A 657 " " NAG A2106 " - " ASN A 709 " " NAG A2107 " - " ASN A1074 " " NAG A2108 " - " ASN A1098 " " NAG A2110 " - " ASN A 282 " " NAG A2111 " - " ASN A 343 " " NAG A2113 " - " ASN A 17 " " NAG A2114 " - " ASN A 61 " " NAG A2115 " - " ASN A 149 " " NAG B2102 " - " ASN B 331 " " NAG B2103 " - " ASN B 603 " " NAG B2104 " - " ASN B 616 " " NAG B2105 " - " ASN B 657 " " NAG B2106 " - " ASN B 709 " " NAG B2107 " - " ASN B1074 " " NAG B2108 " - " ASN B1098 " " NAG B2110 " - " ASN B 282 " " NAG B2111 " - " ASN B 343 " " NAG B2113 " - " ASN B 17 " " NAG B2114 " - " ASN B 61 " " NAG B2115 " - " ASN B 149 " " NAG C2102 " - " ASN C 331 " " NAG C2103 " - " ASN C 603 " " NAG C2104 " - " ASN C 616 " " NAG C2105 " - " ASN C 657 " " NAG C2106 " - " ASN C 709 " " NAG C2107 " - " ASN C1074 " " NAG C2108 " - " ASN C1098 " " NAG C2110 " - " ASN C 282 " " NAG C2111 " - " ASN C 343 " " NAG C2112 " - " ASN C 17 " " NAG C2113 " - " ASN C 61 " " NAG C2114 " - " ASN C 149 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 122 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 122 " Time building additional restraints: 10.14 Conformation dependent library (CDL) restraints added in 5.1 seconds 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 45 sheets defined 21.9% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.90 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 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.250A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) 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 738 through 742 Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.706A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 837 through 841 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.568A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.513A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 943 through 967 removed outlier: 4.959A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 3.571A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.250A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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 738 through 742 Processing helix chain 'B' and resid 747 through 782 removed outlier: 4.706A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 837 through 841 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.568A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 887 through 890 No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.512A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 943 through 967 removed outlier: 4.958A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 3.572A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (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 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.250A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) 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 738 through 742 Processing helix chain 'C' and resid 747 through 782 removed outlier: 4.707A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 837 through 841 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.569A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.512A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 943 through 967 removed outlier: 4.958A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 3.572A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.724A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 56 removed outlier: 3.937A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 242 through 246 removed outlier: 6.546A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= F, first strand: chain 'A' and resid 325 through 328 removed outlier: 8.247A pdb=" N ILE A 326 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.726A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= I, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= J, first strand: chain 'A' and resid 472 through 474 Processing sheet with id= K, first strand: chain 'A' and resid 691 through 696 removed outlier: 5.640A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.939A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1112 through 1114 removed outlier: 4.419A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A1071 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 717 " --> pdb=" O GLN A1071 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS A1073 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A1075 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA A 713 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR A1077 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER A 711 " --> pdb=" O THR A1077 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= P, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.725A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.937A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.547A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= U, first strand: chain 'B' and resid 325 through 328 removed outlier: 8.247A pdb=" N ILE B 326 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.727A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= X, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= Y, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= Z, first strand: chain 'B' and resid 691 through 696 removed outlier: 5.640A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.940A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 1112 through 1114 removed outlier: 4.420A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B1071 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 717 " --> pdb=" O GLN B1071 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS B1073 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE B1075 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA B 713 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B1077 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER B 711 " --> pdb=" O THR B1077 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AE, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 47 through 56 removed outlier: 3.937A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.752A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 242 through 246 removed outlier: 6.547A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= AJ, first strand: chain 'C' and resid 325 through 328 removed outlier: 8.246A pdb=" N ILE C 326 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.726A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AM, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AN, first strand: chain 'C' and resid 472 through 474 Processing sheet with id= AO, first strand: chain 'C' and resid 691 through 696 removed outlier: 5.640A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.940A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 1112 through 1114 removed outlier: 4.419A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C1071 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 717 " --> pdb=" O GLN C1071 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS C1073 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE C1075 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA C 713 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR C1077 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER C 711 " --> pdb=" O THR C1077 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 1088 through 1090 990 hydrogen bonds defined for protein. 2574 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: 11.35 Time building geometry restraints manager: 11.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4351 1.31 - 1.45: 8072 1.45 - 1.58: 14901 1.58 - 1.72: 6 1.72 - 1.86: 144 Bond restraints: 27474 Sorted by residual: bond pdb=" C1C BLA A2101 " pdb=" NC BLA A2101 " ideal model delta sigma weight residual 1.368 1.528 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C1C BLA B2101 " pdb=" NC BLA B2101 " ideal model delta sigma weight residual 1.368 1.527 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C1C BLA C2101 " pdb=" NC BLA C2101 " ideal model delta sigma weight residual 1.368 1.526 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C4C BLA C2101 " pdb=" NC BLA C2101 " ideal model delta sigma weight residual 1.375 1.533 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C4C BLA B2101 " pdb=" NC BLA B2101 " ideal model delta sigma weight residual 1.375 1.532 -0.157 2.00e-02 2.50e+03 6.19e+01 ... (remaining 27469 not shown) Histogram of bond angle deviations from ideal: 97.37 - 107.42: 1511 107.42 - 117.47: 18933 117.47 - 127.52: 16618 127.52 - 137.58: 312 137.58 - 147.63: 3 Bond angle restraints: 37377 Sorted by residual: angle pdb=" CB MET B 902 " pdb=" CG MET B 902 " pdb=" SD MET B 902 " ideal model delta sigma weight residual 112.70 147.63 -34.93 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CB MET C 902 " pdb=" CG MET C 902 " pdb=" SD MET C 902 " ideal model delta sigma weight residual 112.70 147.61 -34.91 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CB MET A 902 " pdb=" CG MET A 902 " pdb=" SD MET A 902 " ideal model delta sigma weight residual 112.70 147.59 -34.89 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG ARG A 273 " pdb=" CD ARG A 273 " pdb=" NE ARG A 273 " ideal model delta sigma weight residual 112.00 136.46 -24.46 2.20e+00 2.07e-01 1.24e+02 angle pdb=" CG ARG C 273 " pdb=" CD ARG C 273 " pdb=" NE ARG C 273 " ideal model delta sigma weight residual 112.00 136.46 -24.46 2.20e+00 2.07e-01 1.24e+02 ... (remaining 37372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16001 17.98 - 35.97: 871 35.97 - 53.95: 288 53.95 - 71.94: 75 71.94 - 89.92: 18 Dihedral angle restraints: 17253 sinusoidal: 7680 harmonic: 9573 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.37 -60.63 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.45 -60.55 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.45 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 17250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4073 0.137 - 0.274: 268 0.274 - 0.412: 30 0.412 - 0.549: 6 0.549 - 0.686: 12 Chirality restraints: 4389 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.61e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.49e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.43e+01 ... (remaining 4386 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A2101 " -0.013 2.00e-02 2.50e+03 8.40e-02 1.76e+02 pdb=" C1D BLA A2101 " 0.191 2.00e-02 2.50e+03 pdb=" C2C BLA A2101 " 0.011 2.00e-02 2.50e+03 pdb=" C3C BLA A2101 " -0.000 2.00e-02 2.50e+03 pdb=" C4C BLA A2101 " -0.078 2.00e-02 2.50e+03 pdb=" CAC BLA A2101 " -0.009 2.00e-02 2.50e+03 pdb=" CHD BLA A2101 " -0.115 2.00e-02 2.50e+03 pdb=" CMC BLA A2101 " 0.094 2.00e-02 2.50e+03 pdb=" NC BLA A2101 " -0.077 2.00e-02 2.50e+03 pdb=" OC BLA A2101 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B2101 " -0.013 2.00e-02 2.50e+03 8.39e-02 1.76e+02 pdb=" C1D BLA B2101 " 0.191 2.00e-02 2.50e+03 pdb=" C2C BLA B2101 " 0.012 2.00e-02 2.50e+03 pdb=" C3C BLA B2101 " -0.001 2.00e-02 2.50e+03 pdb=" C4C BLA B2101 " -0.077 2.00e-02 2.50e+03 pdb=" CAC BLA B2101 " -0.009 2.00e-02 2.50e+03 pdb=" CHD BLA B2101 " -0.115 2.00e-02 2.50e+03 pdb=" CMC BLA B2101 " 0.093 2.00e-02 2.50e+03 pdb=" NC BLA B2101 " -0.077 2.00e-02 2.50e+03 pdb=" OC BLA B2101 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA C2101 " 0.013 2.00e-02 2.50e+03 8.37e-02 1.75e+02 pdb=" C1D BLA C2101 " -0.190 2.00e-02 2.50e+03 pdb=" C2C BLA C2101 " -0.012 2.00e-02 2.50e+03 pdb=" C3C BLA C2101 " 0.001 2.00e-02 2.50e+03 pdb=" C4C BLA C2101 " 0.077 2.00e-02 2.50e+03 pdb=" CAC BLA C2101 " 0.009 2.00e-02 2.50e+03 pdb=" CHD BLA C2101 " 0.114 2.00e-02 2.50e+03 pdb=" CMC BLA C2101 " -0.093 2.00e-02 2.50e+03 pdb=" NC BLA C2101 " 0.077 2.00e-02 2.50e+03 pdb=" OC BLA C2101 " 0.004 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3390 2.74 - 3.28: 25829 3.28 - 3.82: 43716 3.82 - 4.36: 55145 4.36 - 4.90: 93140 Nonbonded interactions: 221220 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.205 2.520 nonbonded pdb=" NZ LYS B 811 " pdb=" OG SER B 813 " model vdw 2.205 2.520 nonbonded pdb=" NZ LYS C 811 " pdb=" OG SER C 813 " model vdw 2.206 2.520 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.256 2.440 ... (remaining 221215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1141 or resid 2101 through 2111 or resid 2113 t \ hrough 2114)) selection = (chain 'B' and (resid 14 through 1141 or resid 2101 through 2111 or resid 2113 t \ hrough 2114)) selection = (chain 'C' and (resid 14 through 1141 or resid 2101 through 2111 or resid 2113 t \ hrough 2114)) } 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.490 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 71.520 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.011 0.160 27474 Z= 0.683 Angle : 1.564 34.927 37377 Z= 0.864 Chirality : 0.085 0.686 4389 Planarity : 0.009 0.084 4746 Dihedral : 12.980 89.920 10968 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 1.05 % Allowed : 1.36 % Favored : 97.59 % Cbeta Deviations : 0.29 % 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: -0.00 (0.13), residues: 3261 helix: 0.28 (0.18), residues: 705 sheet: 0.91 (0.18), residues: 672 loop : -0.41 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 104 HIS 0.045 0.004 HIS B 66 PHE 0.087 0.006 PHE A 220 TYR 0.071 0.003 TYR B 904 ARG 0.041 0.003 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 3.164 Fit side-chains revert: symmetry clash REVERT: A 1073 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: B 153 MET cc_start: 0.6665 (ptt) cc_final: 0.6368 (ptt) REVERT: B 1073 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8115 (mmtp) REVERT: C 220 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7193 (t80) REVERT: C 697 MET cc_start: 0.8403 (ptm) cc_final: 0.8138 (ptm) REVERT: C 985 ASP cc_start: 0.7847 (p0) cc_final: 0.7588 (p0) outliers start: 30 outliers final: 1 residues processed: 286 average time/residue: 0.3974 time to fit residues: 178.1059 Evaluate side-chains 194 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 220 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 256 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 0.0980 chunk 296 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27474 Z= 0.195 Angle : 0.606 6.667 37377 Z= 0.324 Chirality : 0.048 0.480 4389 Planarity : 0.004 0.044 4746 Dihedral : 7.989 62.233 5124 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.73 % Allowed : 3.98 % Favored : 95.28 % 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: 0.40 (0.14), residues: 3261 helix: 1.09 (0.19), residues: 711 sheet: 0.94 (0.18), residues: 675 loop : -0.27 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 152 HIS 0.002 0.001 HIS B 245 PHE 0.023 0.002 PHE B 392 TYR 0.026 0.001 TYR A 904 ARG 0.009 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 2.781 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6660 (ptt) cc_final: 0.6349 (ptt) REVERT: A 1110 TYR cc_start: 0.8351 (t80) cc_final: 0.8135 (t80) REVERT: B 140 PHE cc_start: 0.8419 (p90) cc_final: 0.8110 (p90) REVERT: B 904 TYR cc_start: 0.7594 (m-80) cc_final: 0.7301 (m-80) REVERT: C 140 PHE cc_start: 0.8816 (p90) cc_final: 0.8515 (p90) REVERT: C 153 MET cc_start: 0.6689 (ptt) cc_final: 0.6458 (ptt) outliers start: 21 outliers final: 11 residues processed: 236 average time/residue: 0.3769 time to fit residues: 143.5040 Evaluate side-chains 193 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 658 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 101 optimal weight: 0.0020 chunk 238 optimal weight: 7.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 52 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 27474 Z= 0.479 Angle : 0.670 8.242 37377 Z= 0.352 Chirality : 0.051 0.464 4389 Planarity : 0.005 0.046 4746 Dihedral : 7.032 61.625 5112 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 1.26 % Allowed : 5.84 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3261 helix: 0.47 (0.19), residues: 711 sheet: 0.55 (0.18), residues: 720 loop : -0.37 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 152 HIS 0.006 0.002 HIS A1058 PHE 0.024 0.003 PHE B 759 TYR 0.040 0.002 TYR A 904 ARG 0.007 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 2.852 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.6895 (p0) cc_final: 0.6627 (p0) REVERT: A 731 MET cc_start: 0.9115 (ptt) cc_final: 0.8840 (ptt) REVERT: A 764 ASN cc_start: 0.8867 (m-40) cc_final: 0.8639 (m-40) REVERT: B 378 LYS cc_start: 0.8636 (tttp) cc_final: 0.8414 (ttmt) REVERT: C 80 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.5899 (p0) REVERT: C 153 MET cc_start: 0.6847 (ptt) cc_final: 0.6590 (ptt) REVERT: C 200 TYR cc_start: 0.8803 (m-80) cc_final: 0.8511 (m-80) REVERT: C 228 ASP cc_start: 0.6987 (p0) cc_final: 0.6567 (p0) REVERT: C 902 MET cc_start: 0.8968 (mmm) cc_final: 0.8593 (mmt) REVERT: C 1110 TYR cc_start: 0.8717 (t80) cc_final: 0.8381 (t80) outliers start: 36 outliers final: 29 residues processed: 233 average time/residue: 0.3662 time to fit residues: 140.2909 Evaluate side-chains 193 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1135 ASN C 52 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 954 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27474 Z= 0.328 Angle : 0.557 8.139 37377 Z= 0.291 Chirality : 0.047 0.449 4389 Planarity : 0.004 0.044 4746 Dihedral : 6.444 62.583 5112 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.47 % Allowed : 7.90 % Favored : 90.64 % 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: -0.03 (0.14), residues: 3261 helix: 0.60 (0.20), residues: 714 sheet: 0.51 (0.18), residues: 720 loop : -0.44 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.010 0.001 HIS B 146 PHE 0.016 0.002 PHE C 329 TYR 0.045 0.002 TYR B 904 ARG 0.008 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6654 (ptt) cc_final: 0.6450 (ptt) REVERT: A 228 ASP cc_start: 0.6668 (p0) cc_final: 0.6270 (p0) REVERT: A 764 ASN cc_start: 0.8821 (m-40) cc_final: 0.8611 (m-40) REVERT: A 1002 GLN cc_start: 0.8083 (tt0) cc_final: 0.7858 (tt0) REVERT: B 111 ASP cc_start: 0.7256 (p0) cc_final: 0.6964 (p0) REVERT: B 153 MET cc_start: 0.7760 (pmm) cc_final: 0.7542 (pmm) REVERT: B 228 ASP cc_start: 0.6921 (p0) cc_final: 0.6647 (p0) REVERT: B 378 LYS cc_start: 0.8582 (tttp) cc_final: 0.8318 (ttmm) REVERT: C 66 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6271 (p-80) REVERT: C 111 ASP cc_start: 0.7066 (p0) cc_final: 0.6851 (p0) REVERT: C 200 TYR cc_start: 0.8682 (m-80) cc_final: 0.8376 (m-80) REVERT: C 228 ASP cc_start: 0.6834 (p0) cc_final: 0.6401 (p0) REVERT: C 902 MET cc_start: 0.8905 (mmm) cc_final: 0.8651 (tpt) outliers start: 42 outliers final: 31 residues processed: 228 average time/residue: 0.3839 time to fit residues: 141.9513 Evaluate side-chains 200 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 161 optimal weight: 4.9990 chunk 283 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 764 ASN C 52 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27474 Z= 0.353 Angle : 0.558 7.808 37377 Z= 0.291 Chirality : 0.047 0.428 4389 Planarity : 0.004 0.048 4746 Dihedral : 6.054 62.734 5112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.78 % Allowed : 8.81 % Favored : 89.41 % 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: -0.09 (0.14), residues: 3261 helix: 0.57 (0.20), residues: 714 sheet: 0.52 (0.18), residues: 735 loop : -0.51 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.008 0.001 HIS B 146 PHE 0.014 0.002 PHE B 592 TYR 0.023 0.001 TYR C 904 ARG 0.008 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 185 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.6776 (p0) cc_final: 0.6557 (p0) REVERT: A 985 ASP cc_start: 0.7943 (p0) cc_final: 0.6748 (p0) REVERT: A 1002 GLN cc_start: 0.8101 (tt0) cc_final: 0.7892 (tt0) REVERT: B 153 MET cc_start: 0.7861 (pmm) cc_final: 0.7334 (pmm) REVERT: B 228 ASP cc_start: 0.7016 (p0) cc_final: 0.6752 (p0) REVERT: B 378 LYS cc_start: 0.8596 (tttp) cc_final: 0.8316 (ttmm) REVERT: C 66 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6240 (p-80) REVERT: C 153 MET cc_start: 0.6645 (ptt) cc_final: 0.6435 (ptt) REVERT: C 200 TYR cc_start: 0.8734 (m-80) cc_final: 0.8413 (m-80) REVERT: C 228 ASP cc_start: 0.6953 (p0) cc_final: 0.6538 (p0) outliers start: 51 outliers final: 39 residues processed: 232 average time/residue: 0.3699 time to fit residues: 140.2174 Evaluate side-chains 210 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.6980 chunk 284 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 262 optimal weight: 0.0050 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 137 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 52 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27474 Z= 0.165 Angle : 0.503 9.071 37377 Z= 0.263 Chirality : 0.045 0.403 4389 Planarity : 0.004 0.049 4746 Dihedral : 5.816 63.096 5112 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 9.75 % Favored : 89.17 % 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: 0.11 (0.14), residues: 3261 helix: 0.79 (0.20), residues: 729 sheet: 0.70 (0.18), residues: 729 loop : -0.46 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 152 HIS 0.006 0.000 HIS B 146 PHE 0.015 0.001 PHE B 157 TYR 0.024 0.001 TYR C 904 ARG 0.008 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6533 (ptt) cc_final: 0.6262 (ptt) REVERT: A 228 ASP cc_start: 0.6698 (p0) cc_final: 0.6456 (p0) REVERT: B 65 PHE cc_start: 0.8847 (m-80) cc_final: 0.8552 (m-80) REVERT: B 111 ASP cc_start: 0.7281 (p0) cc_final: 0.6987 (p0) REVERT: B 153 MET cc_start: 0.7806 (pmm) cc_final: 0.7226 (pmm) REVERT: B 228 ASP cc_start: 0.6858 (p0) cc_final: 0.6598 (p0) REVERT: C 66 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6128 (p-80) REVERT: C 153 MET cc_start: 0.6960 (ptt) cc_final: 0.6730 (ptt) REVERT: C 200 TYR cc_start: 0.8628 (m-80) cc_final: 0.8378 (m-80) REVERT: C 228 ASP cc_start: 0.6766 (p0) cc_final: 0.6385 (p0) outliers start: 31 outliers final: 24 residues processed: 205 average time/residue: 0.3696 time to fit residues: 124.5673 Evaluate side-chains 192 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 266 optimal weight: 0.0070 chunk 176 optimal weight: 0.0170 chunk 315 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 0.0670 overall best weight: 0.7776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 137 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27474 Z= 0.157 Angle : 0.480 6.044 37377 Z= 0.252 Chirality : 0.045 0.377 4389 Planarity : 0.004 0.049 4746 Dihedral : 5.497 63.201 5112 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.94 % Allowed : 10.17 % 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: 0.31 (0.14), residues: 3261 helix: 0.97 (0.20), residues: 729 sheet: 0.86 (0.18), residues: 702 loop : -0.33 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.005 0.000 HIS B 146 PHE 0.016 0.001 PHE C 759 TYR 0.020 0.001 TYR C 904 ARG 0.008 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6396 (ptt) cc_final: 0.6178 (ptt) REVERT: A 228 ASP cc_start: 0.6685 (p0) cc_final: 0.6467 (p0) REVERT: A 902 MET cc_start: 0.8807 (tpp) cc_final: 0.8474 (tpp) REVERT: A 904 TYR cc_start: 0.7493 (m-80) cc_final: 0.7271 (m-80) REVERT: B 65 PHE cc_start: 0.8813 (m-80) cc_final: 0.8577 (m-80) REVERT: B 111 ASP cc_start: 0.7315 (p0) cc_final: 0.7063 (p0) REVERT: B 153 MET cc_start: 0.7858 (pmm) cc_final: 0.7203 (pmm) REVERT: B 228 ASP cc_start: 0.6793 (p0) cc_final: 0.6509 (p0) REVERT: C 66 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6153 (p-80) REVERT: C 153 MET cc_start: 0.7034 (ptt) cc_final: 0.6796 (ptt) REVERT: C 200 TYR cc_start: 0.8612 (m-80) cc_final: 0.8259 (m-80) REVERT: C 228 ASP cc_start: 0.6741 (p0) cc_final: 0.6313 (p0) outliers start: 27 outliers final: 23 residues processed: 203 average time/residue: 0.3754 time to fit residues: 125.8891 Evaluate side-chains 199 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27474 Z= 0.178 Angle : 0.477 6.287 37377 Z= 0.250 Chirality : 0.045 0.373 4389 Planarity : 0.004 0.049 4746 Dihedral : 5.395 62.904 5112 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.08 % Allowed : 10.31 % Favored : 88.61 % 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: 0.34 (0.14), residues: 3261 helix: 1.00 (0.20), residues: 729 sheet: 0.85 (0.18), residues: 702 loop : -0.30 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.004 0.001 HIS B 146 PHE 0.015 0.001 PHE B 157 TYR 0.018 0.001 TYR C 365 ARG 0.009 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 2.972 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6465 (ptt) cc_final: 0.6232 (ptt) REVERT: A 228 ASP cc_start: 0.6646 (p0) cc_final: 0.6406 (p0) REVERT: A 904 TYR cc_start: 0.7620 (m-80) cc_final: 0.7392 (m-80) REVERT: B 65 PHE cc_start: 0.8812 (m-80) cc_final: 0.8585 (m-80) REVERT: B 111 ASP cc_start: 0.7320 (p0) cc_final: 0.7073 (p0) REVERT: B 153 MET cc_start: 0.7862 (pmm) cc_final: 0.7163 (pmm) REVERT: B 228 ASP cc_start: 0.6807 (p0) cc_final: 0.6532 (p0) REVERT: C 66 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6210 (p-80) REVERT: C 153 MET cc_start: 0.7067 (ptt) cc_final: 0.6790 (ptt) REVERT: C 200 TYR cc_start: 0.8598 (m-80) cc_final: 0.8259 (m-80) REVERT: C 228 ASP cc_start: 0.6739 (p0) cc_final: 0.6280 (p0) outliers start: 31 outliers final: 25 residues processed: 204 average time/residue: 0.3753 time to fit residues: 126.8136 Evaluate side-chains 196 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 265 optimal weight: 0.1980 chunk 277 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27474 Z= 0.148 Angle : 0.467 5.923 37377 Z= 0.244 Chirality : 0.044 0.364 4389 Planarity : 0.004 0.049 4746 Dihedral : 5.183 62.985 5112 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 10.69 % Favored : 88.23 % 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: 0.41 (0.14), residues: 3261 helix: 1.10 (0.20), residues: 726 sheet: 0.86 (0.18), residues: 702 loop : -0.26 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.004 0.000 HIS B 146 PHE 0.015 0.001 PHE C 759 TYR 0.017 0.001 TYR A 365 ARG 0.010 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6456 (ptt) cc_final: 0.6210 (ptt) REVERT: A 200 TYR cc_start: 0.8520 (m-80) cc_final: 0.8274 (m-80) REVERT: A 228 ASP cc_start: 0.6654 (p0) cc_final: 0.6241 (p0) REVERT: A 902 MET cc_start: 0.8755 (tpp) cc_final: 0.8458 (tpp) REVERT: A 904 TYR cc_start: 0.7700 (m-80) cc_final: 0.7456 (m-80) REVERT: B 111 ASP cc_start: 0.7262 (p0) cc_final: 0.7029 (p0) REVERT: B 228 ASP cc_start: 0.6662 (p0) cc_final: 0.6363 (p0) REVERT: C 66 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6219 (p-80) REVERT: C 153 MET cc_start: 0.6982 (ptt) cc_final: 0.6710 (ptt) REVERT: C 200 TYR cc_start: 0.8576 (m-80) cc_final: 0.8212 (m-80) REVERT: C 212 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8136 (tt) REVERT: C 228 ASP cc_start: 0.6675 (p0) cc_final: 0.6234 (p0) outliers start: 31 outliers final: 27 residues processed: 212 average time/residue: 0.3699 time to fit residues: 128.8001 Evaluate side-chains 204 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 159 optimal weight: 0.0570 chunk 206 optimal weight: 4.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27474 Z= 0.203 Angle : 0.482 5.893 37377 Z= 0.252 Chirality : 0.045 0.365 4389 Planarity : 0.004 0.050 4746 Dihedral : 5.211 62.723 5112 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.29 % Allowed : 10.62 % Favored : 88.09 % 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: 0.38 (0.14), residues: 3261 helix: 1.04 (0.20), residues: 732 sheet: 0.85 (0.18), residues: 702 loop : -0.26 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS B 146 PHE 0.015 0.001 PHE B 157 TYR 0.017 0.001 TYR C 365 ARG 0.010 0.000 ARG C 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 2.963 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6495 (ptt) cc_final: 0.6246 (ptt) REVERT: A 200 TYR cc_start: 0.8548 (m-80) cc_final: 0.8272 (m-80) REVERT: A 228 ASP cc_start: 0.6665 (p0) cc_final: 0.6219 (p0) REVERT: A 731 MET cc_start: 0.9050 (ptt) cc_final: 0.8663 (ptt) REVERT: A 904 TYR cc_start: 0.7715 (m-80) cc_final: 0.7497 (m-80) REVERT: B 111 ASP cc_start: 0.7329 (p0) cc_final: 0.7085 (p0) REVERT: B 153 MET cc_start: 0.7772 (pmm) cc_final: 0.7069 (pmm) REVERT: B 228 ASP cc_start: 0.6773 (p0) cc_final: 0.6497 (p0) REVERT: C 66 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6241 (p-80) REVERT: C 200 TYR cc_start: 0.8589 (m-80) cc_final: 0.8213 (m-80) REVERT: C 212 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (tt) REVERT: C 228 ASP cc_start: 0.6820 (p0) cc_final: 0.6356 (p0) outliers start: 37 outliers final: 31 residues processed: 213 average time/residue: 0.3617 time to fit residues: 127.2623 Evaluate side-chains 207 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 239 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 228 optimal weight: 0.0870 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 901 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083257 restraints weight = 46469.642| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.96 r_work: 0.2839 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 27474 Z= 0.221 Angle : 0.491 14.159 37377 Z= 0.257 Chirality : 0.045 0.366 4389 Planarity : 0.004 0.049 4746 Dihedral : 5.209 62.537 5112 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.33 % Allowed : 10.66 % Favored : 88.02 % 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 (0.14), residues: 3261 helix: 1.09 (0.20), residues: 729 sheet: 0.84 (0.18), residues: 702 loop : -0.28 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS B 146 PHE 0.026 0.001 PHE A 329 TYR 0.018 0.001 TYR B 265 ARG 0.011 0.000 ARG C 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.82 seconds wall clock time: 88 minutes 4.20 seconds (5284.20 seconds total)