Starting phenix.real_space_refine on Mon Feb 19 21:18:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/02_2024/7bbh_12130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/02_2024/7bbh_12130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/02_2024/7bbh_12130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/02_2024/7bbh_12130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/02_2024/7bbh_12130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/02_2024/7bbh_12130.pdb" } resolution = 2.9 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= 0.003 sd= 0.083 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 16431 2.51 5 N 4173 2.21 5 O 5103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 25827 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "B" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 13.51, per 1000 atoms: 0.52 Number of scatterers: 25827 At special positions: 0 Unit cell: (139.062, 130.438, 176.792, 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 5103 8.00 N 4173 7.00 C 16431 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 30 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 122 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 112 " " NAG A1313 " - " ASN A 282 " " NAG A1314 " - " ASN A 657 " " NAG A1315 " - " ASN A1074 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 30 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 122 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 112 " " NAG B1313 " - " ASN B 282 " " NAG B1314 " - " ASN B 657 " " NAG B1315 " - " ASN B1074 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 30 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 112 " " NAG C1313 " - " ASN C 282 " " NAG C1314 " - " ASN C 657 " " NAG C1315 " - " ASN C1074 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 165 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 165 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " Time building additional restraints: 10.70 Conformation dependent library (CDL) restraints added in 5.0 seconds 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 24.8% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.768A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 637 " --> pdb=" O TRP A 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.544A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.002A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.059A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.418A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.948A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.769A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.544A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.609A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.002A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.060A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.419A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.767A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 637 " --> pdb=" O TRP C 633 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.545A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.003A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.060A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.418A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.601A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU A 223 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.262A pdb=" N ASP A 287 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN A 132 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR A 163 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.887A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.422A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 703 removed outlier: 7.201A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A1095 " --> pdb=" O THR A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.602A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU B 223 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.262A pdb=" N ASP B 287 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 132 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 163 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.886A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.422A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 703 removed outlier: 7.128A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B1095 " --> pdb=" O THR B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.601A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU C 223 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.261A pdb=" N ASP C 287 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.684A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN C 132 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C 163 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.886A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.421A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE C1095 " --> pdb=" O THR C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1001 hydrogen bonds defined for protein. 2787 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: 12.13 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8137 1.34 - 1.47: 6639 1.47 - 1.59: 11447 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 26373 Sorted by residual: bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.04e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.85e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.73e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C ALA C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.38e+00 ... (remaining 26368 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 745 106.98 - 113.74: 14865 113.74 - 120.51: 10026 120.51 - 127.27: 10071 127.27 - 134.03: 191 Bond angle restraints: 35898 Sorted by residual: angle pdb=" N PRO C1140 " pdb=" CA PRO C1140 " pdb=" C PRO C1140 " ideal model delta sigma weight residual 112.47 120.19 -7.72 2.06e+00 2.36e-01 1.41e+01 angle pdb=" N PRO B1140 " pdb=" CA PRO B1140 " pdb=" C PRO B1140 " ideal model delta sigma weight residual 112.47 120.18 -7.71 2.06e+00 2.36e-01 1.40e+01 angle pdb=" N PRO A1140 " pdb=" CA PRO A1140 " pdb=" C PRO A1140 " ideal model delta sigma weight residual 112.47 120.17 -7.70 2.06e+00 2.36e-01 1.40e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.51 108.58 4.93 1.52e+00 4.33e-01 1.05e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.51 108.59 4.92 1.52e+00 4.33e-01 1.05e+01 ... (remaining 35893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 15401 17.68 - 35.37: 924 35.37 - 53.05: 187 53.05 - 70.74: 63 70.74 - 88.42: 18 Dihedral angle restraints: 16593 sinusoidal: 7293 harmonic: 9300 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.67 36.67 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.65 36.65 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.62 36.62 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 16590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3236 0.057 - 0.114: 949 0.114 - 0.170: 120 0.170 - 0.227: 3 0.227 - 0.284: 6 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CA PRO B1140 " pdb=" N PRO B1140 " pdb=" C PRO B1140 " pdb=" CB PRO B1140 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PRO C1140 " pdb=" N PRO C1140 " pdb=" C PRO C1140 " pdb=" CB PRO C1140 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO A1140 " pdb=" N PRO A1140 " pdb=" C PRO A1140 " pdb=" CB PRO A1140 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4311 not shown) Planarity restraints: 4590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1139 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO B1140 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1140 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1139 " 0.065 5.00e-02 4.00e+02 9.83e-02 1.55e+01 pdb=" N PRO C1140 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C1140 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1139 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A1140 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A1140 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1140 " -0.052 5.00e-02 4.00e+02 ... (remaining 4587 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6249 2.80 - 3.32: 21591 3.32 - 3.85: 38961 3.85 - 4.37: 47162 4.37 - 4.90: 84244 Nonbonded interactions: 198207 Sorted by model distance: nonbonded pdb=" OD1 ASN C 125 " pdb=" O6 NAG C1304 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASN A 125 " pdb=" O6 NAG A1304 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASN B 125 " pdb=" O6 NAG B1304 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O TYR B 54 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 54 " model vdw 2.316 2.440 ... (remaining 198202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.340 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 72.050 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.260 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 26373 Z= 0.378 Angle : 0.756 9.315 35898 Z= 0.420 Chirality : 0.051 0.284 4314 Planarity : 0.006 0.098 4533 Dihedral : 12.295 88.423 10476 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.86 % Allowed : 3.57 % Favored : 95.57 % 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: -0.97 (0.14), residues: 3129 helix: 0.46 (0.19), residues: 750 sheet: -0.01 (0.19), residues: 726 loop : -1.49 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 886 HIS 0.004 0.001 HIS B1088 PHE 0.023 0.002 PHE A1121 TYR 0.025 0.002 TYR A 265 ARG 0.008 0.001 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 371 time to evaluate : 2.730 Fit side-chains REVERT: A 44 ARG cc_start: 0.7659 (mpp80) cc_final: 0.7303 (mtt180) REVERT: A 100 ILE cc_start: 0.8204 (mm) cc_final: 0.7968 (tt) REVERT: A 370 ASN cc_start: 0.8255 (t0) cc_final: 0.7290 (p0) REVERT: A 633 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.6428 (m100) REVERT: A 690 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7982 (mm110) REVERT: A 836 GLN cc_start: 0.7818 (mt0) cc_final: 0.7467 (mt0) REVERT: B 44 ARG cc_start: 0.7821 (mpp80) cc_final: 0.7447 (mtt180) REVERT: B 370 ASN cc_start: 0.7950 (t0) cc_final: 0.7054 (p0) REVERT: B 529 GLN cc_start: 0.7431 (mt0) cc_final: 0.7225 (mm-40) REVERT: B 633 TRP cc_start: 0.8028 (OUTLIER) cc_final: 0.7024 (m100) REVERT: B 731 MET cc_start: 0.8779 (ptm) cc_final: 0.8558 (ptm) REVERT: C 44 ARG cc_start: 0.7659 (mpp80) cc_final: 0.7096 (mtt180) REVERT: C 54 TYR cc_start: 0.8277 (m-80) cc_final: 0.8038 (m-80) REVERT: C 77 LYS cc_start: 0.7443 (mttt) cc_final: 0.7012 (tptt) REVERT: C 370 ASN cc_start: 0.7733 (t0) cc_final: 0.6754 (p0) REVERT: C 486 PHE cc_start: 0.6996 (t80) cc_final: 0.6728 (t80) REVERT: C 567 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7233 (mtt90) REVERT: C 675 GLN cc_start: 0.6885 (mt0) cc_final: 0.6649 (mp10) REVERT: C 731 MET cc_start: 0.8774 (ptm) cc_final: 0.8283 (ptm) REVERT: C 1101 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.7307 (m90) REVERT: C 1116 THR cc_start: 0.8120 (p) cc_final: 0.7557 (p) outliers start: 24 outliers final: 3 residues processed: 393 average time/residue: 1.3510 time to fit residues: 614.7603 Evaluate side-chains 252 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 151 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 213 ASN A 360 ASN A 388 ASN A 501 ASN A 544 ASN A 804 GLN A 836 GLN A 955 ASN A1010 GLN A1083 HIS A1119 ASN B 132 ASN B 360 ASN B 388 ASN B 501 ASN B 544 ASN B 755 GLN B 804 GLN B1083 HIS B1119 ASN C 125 ASN C 132 ASN C 360 ASN C 388 ASN C 501 ASN C 544 ASN C 755 GLN C 804 GLN C1010 GLN C1083 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26373 Z= 0.228 Angle : 0.582 9.194 35898 Z= 0.316 Chirality : 0.046 0.213 4314 Planarity : 0.005 0.054 4533 Dihedral : 7.154 59.948 4884 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.91 % Allowed : 10.92 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3129 helix: 1.03 (0.20), residues: 753 sheet: 0.46 (0.19), residues: 729 loop : -1.36 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.003 0.001 HIS A1064 PHE 0.018 0.002 PHE C 133 TYR 0.016 0.002 TYR B1067 ARG 0.008 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 256 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7584 (mpp80) cc_final: 0.7115 (mtt180) REVERT: A 100 ILE cc_start: 0.8179 (mm) cc_final: 0.7892 (tt) REVERT: A 370 ASN cc_start: 0.8211 (t0) cc_final: 0.7197 (p0) REVERT: A 633 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.6584 (m100) REVERT: A 675 GLN cc_start: 0.7027 (mt0) cc_final: 0.6456 (mt0) REVERT: A 690 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8053 (mm110) REVERT: A 814 LYS cc_start: 0.6989 (mptt) cc_final: 0.6669 (ptmt) REVERT: A 836 GLN cc_start: 0.7767 (mt0) cc_final: 0.7347 (mt0) REVERT: B 44 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7373 (mtt180) REVERT: B 96 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6155 (pt0) REVERT: B 370 ASN cc_start: 0.8037 (t0) cc_final: 0.7138 (p0) REVERT: B 529 GLN cc_start: 0.7424 (mt0) cc_final: 0.7220 (mm-40) REVERT: B 619 GLU cc_start: 0.7539 (tt0) cc_final: 0.7336 (mt-10) REVERT: B 633 TRP cc_start: 0.8057 (OUTLIER) cc_final: 0.7403 (m100) REVERT: B 690 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8017 (mm-40) REVERT: B 836 GLN cc_start: 0.7607 (mt0) cc_final: 0.7384 (mt0) REVERT: C 44 ARG cc_start: 0.7747 (mpp80) cc_final: 0.7077 (mtt180) REVERT: C 54 TYR cc_start: 0.8288 (m-80) cc_final: 0.8071 (m-80) REVERT: C 96 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6636 (pt0) REVERT: C 357 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7660 (tpt-90) REVERT: C 370 ASN cc_start: 0.7920 (t0) cc_final: 0.6969 (p0) REVERT: C 521 PRO cc_start: 0.8688 (Cg_endo) cc_final: 0.8452 (Cg_exo) REVERT: C 567 ARG cc_start: 0.7585 (mtt90) cc_final: 0.7322 (mtt90) REVERT: C 731 MET cc_start: 0.8833 (ptm) cc_final: 0.8402 (ptm) REVERT: C 836 GLN cc_start: 0.7546 (mt0) cc_final: 0.7122 (mt0) REVERT: C 1101 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7317 (m90) outliers start: 53 outliers final: 21 residues processed: 287 average time/residue: 1.3027 time to fit residues: 436.9517 Evaluate side-chains 251 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 804 GLN A 955 ASN A1010 GLN B 755 GLN B 955 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26373 Z= 0.217 Angle : 0.557 7.821 35898 Z= 0.299 Chirality : 0.045 0.215 4314 Planarity : 0.004 0.038 4533 Dihedral : 6.868 59.849 4880 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.92 % Allowed : 11.86 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 3129 helix: 1.25 (0.20), residues: 756 sheet: 0.64 (0.19), residues: 720 loop : -1.35 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.015 0.001 PHE C 133 TYR 0.016 0.001 TYR B1067 ARG 0.006 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 232 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7622 (mpp80) cc_final: 0.7204 (mtt180) REVERT: A 96 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6750 (pt0) REVERT: A 370 ASN cc_start: 0.8218 (t0) cc_final: 0.7201 (p0) REVERT: A 633 TRP cc_start: 0.7991 (OUTLIER) cc_final: 0.6368 (m100) REVERT: A 675 GLN cc_start: 0.7005 (mt0) cc_final: 0.6702 (mt0) REVERT: A 690 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8168 (mm110) REVERT: A 697 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8326 (ptp) REVERT: A 814 LYS cc_start: 0.6976 (mptt) cc_final: 0.6672 (ptmt) REVERT: A 836 GLN cc_start: 0.7774 (mt0) cc_final: 0.7367 (mt0) REVERT: A 964 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7677 (ttmm) REVERT: B 96 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6162 (pt0) REVERT: B 370 ASN cc_start: 0.8096 (t0) cc_final: 0.7199 (p0) REVERT: B 633 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7302 (m100) REVERT: C 44 ARG cc_start: 0.7794 (mpp80) cc_final: 0.7071 (mtt180) REVERT: C 54 TYR cc_start: 0.8309 (m-80) cc_final: 0.8043 (m-80) REVERT: C 96 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: C 357 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7581 (tpt-90) REVERT: C 370 ASN cc_start: 0.8115 (t0) cc_final: 0.7282 (p0) REVERT: C 567 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7358 (mtt90) REVERT: C 697 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8329 (ptp) REVERT: C 814 LYS cc_start: 0.7027 (mptt) cc_final: 0.6503 (ptmt) REVERT: C 836 GLN cc_start: 0.7561 (mt0) cc_final: 0.7201 (mt0) REVERT: C 866 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8220 (m) REVERT: C 1101 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7303 (m90) outliers start: 81 outliers final: 39 residues processed: 291 average time/residue: 1.3468 time to fit residues: 457.6687 Evaluate side-chains 266 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.0470 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 955 ASN A1010 GLN B 213 ASN B 690 GLN B 755 GLN B 955 ASN C 544 ASN C 690 GLN C 755 GLN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26373 Z= 0.204 Angle : 0.541 9.145 35898 Z= 0.288 Chirality : 0.045 0.213 4314 Planarity : 0.004 0.039 4533 Dihedral : 6.719 59.210 4880 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.45 % Allowed : 13.55 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.20 (0.15), residues: 3129 helix: 1.38 (0.20), residues: 756 sheet: 0.81 (0.19), residues: 714 loop : -1.35 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS C1088 PHE 0.014 0.001 PHE C 643 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 227 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6657 (pt0) REVERT: A 218 ILE cc_start: 0.8345 (mp) cc_final: 0.8123 (mt) REVERT: A 370 ASN cc_start: 0.8213 (t0) cc_final: 0.7202 (p0) REVERT: A 633 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.6206 (m100) REVERT: A 675 GLN cc_start: 0.7059 (mt0) cc_final: 0.6764 (mt0) REVERT: A 690 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8125 (mm110) REVERT: A 697 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8375 (ptp) REVERT: A 814 LYS cc_start: 0.6964 (mptt) cc_final: 0.6648 (ptmt) REVERT: A 836 GLN cc_start: 0.7742 (mt0) cc_final: 0.7377 (mt0) REVERT: A 964 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7643 (ttmm) REVERT: B 96 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6166 (pt0) REVERT: B 370 ASN cc_start: 0.8101 (t0) cc_final: 0.7209 (p0) REVERT: B 633 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.7278 (m100) REVERT: B 866 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7977 (m) REVERT: C 44 ARG cc_start: 0.7843 (mpp80) cc_final: 0.7035 (mtt180) REVERT: C 54 TYR cc_start: 0.8297 (m-80) cc_final: 0.7961 (m-80) REVERT: C 96 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: C 97 LYS cc_start: 0.7952 (ptpp) cc_final: 0.7746 (ptpp) REVERT: C 357 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7462 (tpt-90) REVERT: C 370 ASN cc_start: 0.8129 (t0) cc_final: 0.7279 (p0) REVERT: C 697 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8336 (ptp) REVERT: C 866 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8158 (m) REVERT: C 964 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7680 (ttmm) REVERT: C 1101 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7353 (m90) outliers start: 68 outliers final: 37 residues processed: 277 average time/residue: 1.2920 time to fit residues: 419.5755 Evaluate side-chains 262 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 228 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 77 optimal weight: 0.0000 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 955 ASN B 544 ASN B 690 GLN B 755 GLN B 955 ASN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26373 Z= 0.299 Angle : 0.598 10.403 35898 Z= 0.318 Chirality : 0.047 0.225 4314 Planarity : 0.004 0.039 4533 Dihedral : 6.792 59.196 4880 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.92 % Allowed : 13.77 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3129 helix: 1.05 (0.19), residues: 777 sheet: 0.71 (0.20), residues: 699 loop : -1.45 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.018 0.002 PHE A1121 TYR 0.016 0.002 TYR A1067 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 228 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7657 (ptp90) REVERT: A 96 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6722 (pt0) REVERT: A 370 ASN cc_start: 0.8261 (t0) cc_final: 0.7251 (p0) REVERT: A 633 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.6254 (m100) REVERT: A 690 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8042 (mm110) REVERT: A 697 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8358 (ptp) REVERT: A 814 LYS cc_start: 0.7019 (mptt) cc_final: 0.6810 (ptmm) REVERT: A 836 GLN cc_start: 0.7773 (mt0) cc_final: 0.7400 (mt0) REVERT: B 96 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: B 357 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7412 (tpt-90) REVERT: B 370 ASN cc_start: 0.8139 (t0) cc_final: 0.7230 (p0) REVERT: B 633 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.7218 (m100) REVERT: B 697 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8340 (ptp) REVERT: B 900 MET cc_start: 0.8288 (mtt) cc_final: 0.7718 (mtt) REVERT: C 44 ARG cc_start: 0.7890 (mpp80) cc_final: 0.6955 (mtt180) REVERT: C 54 TYR cc_start: 0.8241 (m-80) cc_final: 0.8024 (m-80) REVERT: C 357 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7920 (tpt170) REVERT: C 370 ASN cc_start: 0.8173 (t0) cc_final: 0.7288 (p0) REVERT: C 567 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6417 (mtt90) REVERT: C 633 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7843 (m100) REVERT: C 697 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8367 (ptp) REVERT: C 836 GLN cc_start: 0.7520 (mt0) cc_final: 0.7289 (mt0) REVERT: C 866 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8185 (m) REVERT: C 964 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7717 (ttmm) REVERT: C 1038 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7692 (mmtt) REVERT: C 1101 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7412 (m90) outliers start: 81 outliers final: 41 residues processed: 287 average time/residue: 1.2382 time to fit residues: 417.4097 Evaluate side-chains 266 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 955 ASN B 690 GLN B 755 GLN B 955 ASN C 755 GLN C1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26373 Z= 0.321 Angle : 0.617 14.703 35898 Z= 0.327 Chirality : 0.047 0.233 4314 Planarity : 0.005 0.040 4533 Dihedral : 6.904 59.906 4880 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.24 % Allowed : 14.34 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.51 (0.14), residues: 3129 helix: 0.94 (0.19), residues: 777 sheet: 0.66 (0.20), residues: 702 loop : -1.48 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.018 0.002 PHE A1121 TYR 0.017 0.002 TYR A1067 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 216 time to evaluate : 3.265 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7638 (ptp90) REVERT: A 52 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: A 96 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6847 (pt0) REVERT: A 218 ILE cc_start: 0.8463 (mp) cc_final: 0.8247 (mt) REVERT: A 370 ASN cc_start: 0.8344 (t0) cc_final: 0.7504 (p0) REVERT: A 633 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.6293 (m100) REVERT: A 690 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7994 (mm110) REVERT: A 697 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8356 (ptp) REVERT: A 836 GLN cc_start: 0.7768 (mt0) cc_final: 0.7401 (mt0) REVERT: B 96 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6351 (pt0) REVERT: B 357 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7423 (tpt-90) REVERT: B 370 ASN cc_start: 0.8163 (t0) cc_final: 0.7243 (p0) REVERT: B 633 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.7252 (m100) REVERT: B 900 MET cc_start: 0.8288 (mtt) cc_final: 0.7714 (mtt) REVERT: C 44 ARG cc_start: 0.7947 (mpp80) cc_final: 0.7108 (mtt180) REVERT: C 54 TYR cc_start: 0.8234 (m-80) cc_final: 0.7983 (m-80) REVERT: C 357 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7690 (tpt-90) REVERT: C 370 ASN cc_start: 0.8195 (t0) cc_final: 0.7302 (p0) REVERT: C 633 TRP cc_start: 0.8133 (OUTLIER) cc_final: 0.7768 (m100) REVERT: C 697 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8390 (ptp) REVERT: C 866 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8155 (m) REVERT: C 964 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7740 (ttmm) REVERT: C 1038 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7692 (mmtt) outliers start: 90 outliers final: 51 residues processed: 289 average time/residue: 1.2180 time to fit residues: 416.8145 Evaluate side-chains 274 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 209 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 186 optimal weight: 0.0570 chunk 141 optimal weight: 0.3980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 215 ASN B 544 ASN B 755 GLN B 955 ASN C 132 ASN C 493 GLN C 544 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 26373 Z= 0.152 Angle : 0.520 12.263 35898 Z= 0.276 Chirality : 0.044 0.217 4314 Planarity : 0.004 0.038 4533 Dihedral : 6.441 58.325 4878 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.20 % Allowed : 15.50 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.21 (0.15), residues: 3129 helix: 1.46 (0.20), residues: 753 sheet: 0.82 (0.20), residues: 720 loop : -1.41 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.002 0.000 HIS C1088 PHE 0.017 0.001 PHE B 643 TYR 0.016 0.001 TYR A1067 ARG 0.008 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 227 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7575 (ptp90) REVERT: A 52 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7483 (tp40) REVERT: A 96 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6677 (pt0) REVERT: A 370 ASN cc_start: 0.8173 (t0) cc_final: 0.7180 (p0) REVERT: A 633 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.6265 (m100) REVERT: A 690 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7958 (mm110) REVERT: A 836 GLN cc_start: 0.7770 (mt0) cc_final: 0.7396 (mt0) REVERT: B 96 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6232 (pt0) REVERT: B 99 ASN cc_start: 0.7006 (p0) cc_final: 0.6013 (m-40) REVERT: B 370 ASN cc_start: 0.8108 (t0) cc_final: 0.7224 (p0) REVERT: B 633 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7292 (m100) REVERT: B 697 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8348 (ptp) REVERT: B 866 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7930 (m) REVERT: B 900 MET cc_start: 0.8141 (mtt) cc_final: 0.7629 (mtt) REVERT: C 44 ARG cc_start: 0.7914 (mpp80) cc_final: 0.7094 (mtt180) REVERT: C 54 TYR cc_start: 0.8197 (m-80) cc_final: 0.7931 (m-80) REVERT: C 370 ASN cc_start: 0.8144 (t0) cc_final: 0.7289 (p0) REVERT: C 567 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6568 (mtt90) REVERT: C 633 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7701 (m100) REVERT: C 675 GLN cc_start: 0.6943 (mt0) cc_final: 0.6573 (mp10) REVERT: C 964 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7674 (ttmm) outliers start: 61 outliers final: 29 residues processed: 274 average time/residue: 1.2047 time to fit residues: 391.9245 Evaluate side-chains 255 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 544 ASN B 755 GLN B 955 ASN B1135 ASN C 544 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26373 Z= 0.301 Angle : 0.601 12.862 35898 Z= 0.318 Chirality : 0.047 0.238 4314 Planarity : 0.004 0.040 4533 Dihedral : 6.665 59.902 4878 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.52 % Allowed : 15.57 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.42 (0.15), residues: 3129 helix: 1.08 (0.19), residues: 774 sheet: 0.65 (0.20), residues: 696 loop : -1.42 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.018 0.002 PHE A1121 TYR 0.016 0.002 TYR A1067 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 212 time to evaluate : 3.320 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7542 (ptp90) REVERT: A 52 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7546 (tp40) REVERT: A 96 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: A 218 ILE cc_start: 0.8454 (mp) cc_final: 0.8215 (mt) REVERT: A 370 ASN cc_start: 0.8273 (t0) cc_final: 0.7455 (p0) REVERT: A 633 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.6222 (m100) REVERT: A 690 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7948 (mm110) REVERT: A 697 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8372 (ptp) REVERT: A 836 GLN cc_start: 0.7790 (mt0) cc_final: 0.7402 (mt0) REVERT: A 1038 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7571 (mmtt) REVERT: B 96 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6361 (pt0) REVERT: B 357 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7348 (tpt-90) REVERT: B 370 ASN cc_start: 0.8144 (t0) cc_final: 0.7235 (p0) REVERT: B 633 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7298 (m100) REVERT: B 964 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (mtmm) REVERT: C 44 ARG cc_start: 0.7905 (mpp80) cc_final: 0.7059 (mtt180) REVERT: C 54 TYR cc_start: 0.8216 (m-80) cc_final: 0.7957 (m-80) REVERT: C 357 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7490 (tpt-90) REVERT: C 370 ASN cc_start: 0.8178 (t0) cc_final: 0.7292 (p0) REVERT: C 567 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6480 (mtt90) REVERT: C 633 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7758 (m100) REVERT: C 697 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8395 (ptp) REVERT: C 836 GLN cc_start: 0.7561 (mt0) cc_final: 0.7293 (mt0) REVERT: C 866 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8117 (m) REVERT: C 964 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7707 (ttmm) REVERT: C 1038 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7611 (mmtt) outliers start: 70 outliers final: 41 residues processed: 268 average time/residue: 1.2457 time to fit residues: 394.8930 Evaluate side-chains 266 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9980 chunk 293 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 285 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 224 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 0.0970 chunk 270 optimal weight: 0.5980 chunk 284 optimal weight: 0.0020 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 ASN B 755 GLN B 787 GLN B 901 GLN B 955 ASN C 544 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26373 Z= 0.143 Angle : 0.511 10.656 35898 Z= 0.270 Chirality : 0.043 0.217 4314 Planarity : 0.004 0.039 4533 Dihedral : 6.276 58.235 4878 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.87 % Allowed : 16.61 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.18 (0.15), residues: 3129 helix: 1.56 (0.20), residues: 750 sheet: 0.75 (0.20), residues: 714 loop : -1.38 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.002 0.000 HIS B1088 PHE 0.014 0.001 PHE B 643 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6375 (pt0) REVERT: A 218 ILE cc_start: 0.8395 (mp) cc_final: 0.8169 (mt) REVERT: A 370 ASN cc_start: 0.8180 (t0) cc_final: 0.7337 (p0) REVERT: A 633 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.6345 (m100) REVERT: A 690 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7926 (mm110) REVERT: A 697 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8379 (ptp) REVERT: A 836 GLN cc_start: 0.7750 (mt0) cc_final: 0.7414 (mt0) REVERT: B 96 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6280 (pt0) REVERT: B 370 ASN cc_start: 0.8106 (t0) cc_final: 0.7223 (p0) REVERT: B 633 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7342 (m100) REVERT: B 866 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7938 (m) REVERT: C 44 ARG cc_start: 0.7861 (mpp80) cc_final: 0.7043 (mtt180) REVERT: C 54 TYR cc_start: 0.8162 (m-80) cc_final: 0.7895 (m-80) REVERT: C 370 ASN cc_start: 0.8149 (t0) cc_final: 0.7287 (p0) REVERT: C 633 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7752 (m100) REVERT: C 697 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8341 (ptp) REVERT: C 866 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8075 (m) REVERT: C 933 LYS cc_start: 0.8122 (mttt) cc_final: 0.7775 (mtpm) outliers start: 52 outliers final: 29 residues processed: 259 average time/residue: 1.2254 time to fit residues: 376.5399 Evaluate side-chains 249 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 211 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 0.0870 chunk 316 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 544 ASN B 755 GLN B 787 GLN B 901 GLN B 955 ASN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26373 Z= 0.191 Angle : 0.536 10.604 35898 Z= 0.283 Chirality : 0.044 0.225 4314 Planarity : 0.004 0.040 4533 Dihedral : 6.278 58.226 4878 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.55 % Allowed : 16.97 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.21 (0.15), residues: 3129 helix: 1.48 (0.20), residues: 756 sheet: 0.75 (0.20), residues: 714 loop : -1.38 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.002 0.001 HIS B1064 PHE 0.018 0.001 PHE C 643 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6353 (pt0) REVERT: A 370 ASN cc_start: 0.8240 (t0) cc_final: 0.7423 (p0) REVERT: A 633 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.6369 (m100) REVERT: A 690 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8161 (mm-40) REVERT: A 697 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8386 (ptp) REVERT: A 836 GLN cc_start: 0.7753 (mt0) cc_final: 0.7412 (mt0) REVERT: B 96 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6370 (pt0) REVERT: B 370 ASN cc_start: 0.8109 (t0) cc_final: 0.7226 (p0) REVERT: B 633 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7356 (m100) REVERT: C 44 ARG cc_start: 0.7925 (mpp80) cc_final: 0.7108 (mtt180) REVERT: C 54 TYR cc_start: 0.8143 (m-80) cc_final: 0.7863 (m-80) REVERT: C 370 ASN cc_start: 0.8146 (t0) cc_final: 0.7277 (p0) REVERT: C 567 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6616 (mtt90) REVERT: C 633 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7688 (m100) REVERT: C 675 GLN cc_start: 0.7076 (mt0) cc_final: 0.6730 (mp10) REVERT: C 697 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8357 (ptp) REVERT: C 866 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8088 (m) REVERT: C 933 LYS cc_start: 0.8009 (mttt) cc_final: 0.7748 (mtpm) outliers start: 43 outliers final: 29 residues processed: 246 average time/residue: 1.1817 time to fit residues: 344.4579 Evaluate side-chains 245 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 232 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 252 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 544 ASN B 755 GLN B 787 GLN B 901 GLN B 955 ASN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126621 restraints weight = 30040.103| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.13 r_work: 0.3325 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26373 Z= 0.160 Angle : 0.515 9.967 35898 Z= 0.271 Chirality : 0.044 0.218 4314 Planarity : 0.004 0.039 4533 Dihedral : 6.126 57.731 4878 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.73 % Allowed : 16.86 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.13 (0.15), residues: 3129 helix: 1.64 (0.20), residues: 741 sheet: 0.76 (0.20), residues: 714 loop : -1.34 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 886 HIS 0.002 0.001 HIS C1064 PHE 0.015 0.001 PHE B 643 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7829.84 seconds wall clock time: 140 minutes 44.86 seconds (8444.86 seconds total)