Starting phenix.real_space_refine on Mon Feb 19 18:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm3_22254/02_2024/6xm3_22254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm3_22254/02_2024/6xm3_22254.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/6xm3_22254/02_2024/6xm3_22254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm3_22254/02_2024/6xm3_22254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm3_22254/02_2024/6xm3_22254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm3_22254/02_2024/6xm3_22254.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= -0.000 sd= 0.965 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 110 5.16 5 C 16148 2.51 5 N 4142 2.21 5 O 4984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C TYR 200": "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 ARG 273": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1107": "NH1" <-> "NH2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" 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: 25384 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8111 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain breaks: 7 Chain: "B" Number of atoms: 8259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 bond proxies already assigned to first conformer: 8435 Chain: "C" Number of atoms: 8174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8174 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 52, 'TRANS': 994} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "T" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.54, per 1000 atoms: 0.69 Number of scatterers: 25384 At special positions: 0 Unit cell: (140.25, 136, 199.75, 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 110 16.00 O 4984 8.00 N 4142 7.00 C 16148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 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=2.03 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.02 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 10.09 Conformation dependent library (CDL) restraints added in 6.4 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 44 sheets defined 24.2% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.503A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.613A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.686A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.698A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.569A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.741A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.896A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.557A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.559A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.560A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.979A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.603A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.511A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.605A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.733A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.605A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (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 982 removed outlier: 3.684A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.747A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.565A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.632A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.509A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 806 Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 839 removed outlier: 3.554A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.636A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.762A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.655A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 935 removed outlier: 3.513A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 981 removed outlier: 3.605A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.135A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.553A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.124A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.891A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.522A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 removed outlier: 4.018A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.610A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.636A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 removed outlier: 3.637A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 removed outlier: 3.545A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.531A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.803A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.691A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.611A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.537A 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 982 Processing helix chain 'C' and resid 985 through 989 Processing helix chain 'C' and resid 992 through 1032 removed outlier: 3.754A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.014A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.439A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.256A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.671A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 3.978A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.585A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.834A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.012A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.391A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.470A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.210A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.860A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.295A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.001A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.657A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.744A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.684A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.021A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.790A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.535A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.669A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.679A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.066A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.795A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.545A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.640A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.544A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.609A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.609A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 836 hydrogen bonds defined for protein. 2250 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: 12.38 Time building geometry restraints manager: 10.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7554 1.33 - 1.46: 7080 1.46 - 1.60: 11176 1.60 - 1.73: 1 1.73 - 1.86: 134 Bond restraints: 25945 Sorted by residual: bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.20e-02 6.94e+03 1.39e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.201 0.040 1.12e-02 7.97e+03 1.26e+01 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.06e-02 8.90e+03 1.18e+01 bond pdb=" C LYS B 790 " pdb=" N THR B 791 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.03e+01 bond pdb=" C ASP B 808 " pdb=" N PRO B 809 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.06e-02 8.90e+03 9.79e+00 ... (remaining 25940 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.93: 470 104.93 - 112.27: 12799 112.27 - 119.60: 9153 119.60 - 126.94: 12645 126.94 - 134.28: 254 Bond angle restraints: 35321 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.30 99.46 13.84 1.34e+00 5.57e-01 1.07e+02 angle pdb=" C ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta sigma weight residual 109.83 119.71 -9.88 9.90e-01 1.02e+00 9.95e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.23e+00 6.61e-01 5.56e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 angle pdb=" CA VAL B 620 " pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 120.83 124.32 -3.49 6.10e-01 2.69e+00 3.28e+01 ... (remaining 35316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 14512 17.50 - 35.00: 1324 35.00 - 52.50: 304 52.50 - 70.00: 64 70.00 - 87.49: 31 Dihedral angle restraints: 16235 sinusoidal: 7074 harmonic: 9161 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 176.60 -83.60 1 1.00e+01 1.00e-02 8.53e+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 93.00 161.11 -68.11 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -30.58 -55.42 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 16232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3527 0.095 - 0.189: 614 0.189 - 0.284: 49 0.284 - 0.378: 4 0.378 - 0.473: 6 Chirality restraints: 4200 Sorted by residual: chirality pdb=" CA ASN B 616 " pdb=" N ASN B 616 " pdb=" C ASN B 616 " pdb=" CB ASN B 616 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 4197 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 987 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 393 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C THR A 393 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 393 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 394 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.020 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE C 906 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.002 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5127 2.77 - 3.30: 20566 3.30 - 3.83: 39415 3.83 - 4.37: 46372 4.37 - 4.90: 82677 Nonbonded interactions: 194157 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.233 2.440 nonbonded pdb=" O GLN A 134 " pdb=" OH TYR A 160 " model vdw 2.252 2.440 nonbonded pdb=" O LEU B 293 " pdb=" OG1 THR B 632 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.265 2.440 nonbonded pdb=" O GLN C 134 " pdb=" OH TYR C 160 " model vdw 2.266 2.440 ... (remaining 194152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 492 or resid 494 through 848 or resid 850 through 1147 or resid 1301 through \ 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 444 or resid 447 throu \ gh 492 or resid 494 through 828 or resid 848 or resid 850 through 1147 or resid \ 1301 through 1308)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 492 or resid 494 throu \ gh 828 or resid 830 or resid 834 or resid 851 through 1147 or resid 1301 through \ 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 5.530 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: 19.390 Check model and map are aligned: 0.360 Set scattering table: 0.250 Process input model: 76.880 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.013 0.137 25945 Z= 0.812 Angle : 1.035 13.975 35321 Z= 0.571 Chirality : 0.071 0.473 4200 Planarity : 0.008 0.104 4493 Dihedral : 14.378 87.494 10214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 0.66 % Allowed : 6.37 % Favored : 92.97 % Cbeta Deviations : 0.10 % 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: -4.38 (0.12), residues: 3100 helix: -4.55 (0.08), residues: 672 sheet: -1.28 (0.19), residues: 705 loop : -3.00 (0.12), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 886 HIS 0.011 0.002 HIS C1048 PHE 0.054 0.003 PHE C 906 TYR 0.034 0.003 TYR B 904 ARG 0.004 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6850 (mtmm) REVERT: A 351 TYR cc_start: 0.8090 (p90) cc_final: 0.7682 (p90) REVERT: A 365 TYR cc_start: 0.8053 (m-80) cc_final: 0.7735 (m-80) REVERT: A 378 LYS cc_start: 0.7585 (tttm) cc_final: 0.6897 (tmtt) REVERT: A 385 THR cc_start: 0.8488 (m) cc_final: 0.8245 (p) REVERT: A 403 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7316 (ttm-80) REVERT: A 417 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7343 (mtpt) REVERT: A 420 ASP cc_start: 0.7937 (m-30) cc_final: 0.7542 (m-30) REVERT: A 505 TYR cc_start: 0.7701 (m-80) cc_final: 0.7484 (m-80) REVERT: A 773 GLU cc_start: 0.8145 (tt0) cc_final: 0.7767 (tt0) REVERT: A 904 TYR cc_start: 0.7612 (m-80) cc_final: 0.7234 (m-80) REVERT: A 1086 LYS cc_start: 0.8406 (mmpt) cc_final: 0.8136 (mtpt) REVERT: B 218 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8312 (mm-40) REVERT: B 396 TYR cc_start: 0.7445 (m-80) cc_final: 0.7039 (m-80) REVERT: B 613 GLN cc_start: 0.7621 (mt0) cc_final: 0.6962 (pt0) REVERT: B 635 VAL cc_start: 0.8125 (t) cc_final: 0.7831 (m) REVERT: B 850 ILE cc_start: 0.8167 (mp) cc_final: 0.7797 (mm) REVERT: B 1125 ASN cc_start: 0.7939 (m-40) cc_final: 0.7585 (t0) REVERT: B 1138 TYR cc_start: 0.7816 (t80) cc_final: 0.7517 (t80) REVERT: C 190 ARG cc_start: 0.5823 (mtt-85) cc_final: 0.4879 (ttp-170) REVERT: C 273 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7208 (mmt-90) REVERT: C 319 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7658 (ttm110) REVERT: C 357 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7648 (ttt-90) REVERT: C 430 THR cc_start: 0.8416 (t) cc_final: 0.8210 (m) REVERT: C 603 ASN cc_start: 0.8640 (t0) cc_final: 0.8364 (t0) REVERT: C 1092 GLU cc_start: 0.7289 (mp0) cc_final: 0.6876 (pp20) outliers start: 16 outliers final: 6 residues processed: 267 average time/residue: 1.2772 time to fit residues: 399.1287 Evaluate side-chains 181 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.1980 chunk 236 optimal weight: 0.0770 chunk 131 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 0.0270 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 8.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 439 ASN A 580 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 901 GLN A 954 GLN B 30 ASN B 134 GLN B 137 ASN B 211 ASN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 556 ASN B 675 GLN B 690 GLN B 901 GLN C 87 ASN C 211 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 25945 Z= 0.156 Angle : 0.620 24.909 35321 Z= 0.319 Chirality : 0.046 0.306 4200 Planarity : 0.005 0.076 4493 Dihedral : 7.724 59.922 4633 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.78 % Allowed : 10.05 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.13), residues: 3100 helix: -2.15 (0.17), residues: 673 sheet: -0.47 (0.20), residues: 652 loop : -2.46 (0.12), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 886 HIS 0.002 0.000 HIS A 519 PHE 0.020 0.001 PHE B 377 TYR 0.026 0.001 TYR B 904 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 210 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6576 (mtmm) REVERT: A 351 TYR cc_start: 0.8096 (p90) cc_final: 0.7695 (p90) REVERT: A 403 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7446 (ttm-80) REVERT: A 417 LYS cc_start: 0.7546 (mtmt) cc_final: 0.7121 (mtpt) REVERT: A 420 ASP cc_start: 0.7768 (m-30) cc_final: 0.7402 (m-30) REVERT: A 462 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7577 (mppt) REVERT: A 505 TYR cc_start: 0.7598 (m-80) cc_final: 0.7387 (m-80) REVERT: A 563 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.4739 (mp10) REVERT: A 773 GLU cc_start: 0.7865 (tt0) cc_final: 0.7591 (tt0) REVERT: A 904 TYR cc_start: 0.7406 (m-80) cc_final: 0.7156 (m-80) REVERT: A 1086 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8258 (mtpt) REVERT: B 237 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7173 (mtm-85) REVERT: B 396 TYR cc_start: 0.7333 (m-80) cc_final: 0.6922 (m-80) REVERT: B 613 GLN cc_start: 0.7471 (mt0) cc_final: 0.6886 (pt0) REVERT: B 635 VAL cc_start: 0.8009 (t) cc_final: 0.7720 (m) REVERT: B 826 VAL cc_start: 0.8884 (p) cc_final: 0.8601 (t) REVERT: B 850 ILE cc_start: 0.8007 (mp) cc_final: 0.7703 (mm) REVERT: B 988 GLU cc_start: 0.7388 (mp0) cc_final: 0.6720 (mp0) REVERT: B 1125 ASN cc_start: 0.7825 (m-40) cc_final: 0.7458 (t0) REVERT: B 1138 TYR cc_start: 0.7745 (t80) cc_final: 0.7469 (t80) REVERT: C 205 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8758 (t) REVERT: C 357 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7471 (ttt-90) REVERT: C 505 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6184 (t80) REVERT: C 603 ASN cc_start: 0.8509 (t0) cc_final: 0.8262 (t0) REVERT: C 646 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7428 (mtp180) outliers start: 47 outliers final: 12 residues processed: 239 average time/residue: 1.1915 time to fit residues: 336.5328 Evaluate side-chains 190 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 644 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25945 Z= 0.297 Angle : 0.657 22.721 35321 Z= 0.334 Chirality : 0.049 0.285 4200 Planarity : 0.005 0.076 4493 Dihedral : 7.147 58.906 4627 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.40 % Allowed : 11.84 % Favored : 85.76 % 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: -2.25 (0.14), residues: 3100 helix: -1.00 (0.20), residues: 688 sheet: -0.19 (0.20), residues: 674 loop : -2.34 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.009 0.001 HIS B1064 PHE 0.020 0.002 PHE A 592 TYR 0.031 0.002 TYR B 904 ARG 0.011 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 182 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7236 (pp20) cc_final: 0.6998 (pp20) REVERT: A 129 LYS cc_start: 0.6917 (mtpp) cc_final: 0.6541 (mtmm) REVERT: A 351 TYR cc_start: 0.8214 (p90) cc_final: 0.7888 (p90) REVERT: A 417 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7309 (mtpt) REVERT: A 420 ASP cc_start: 0.7747 (m-30) cc_final: 0.7340 (m-30) REVERT: A 563 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.4765 (mp10) REVERT: A 773 GLU cc_start: 0.7997 (tt0) cc_final: 0.7618 (tt0) REVERT: A 1086 LYS cc_start: 0.8492 (mmpt) cc_final: 0.8178 (mtpt) REVERT: B 396 TYR cc_start: 0.7359 (m-80) cc_final: 0.7111 (m-80) REVERT: B 613 GLN cc_start: 0.7516 (mt0) cc_final: 0.6908 (pt0) REVERT: B 635 VAL cc_start: 0.8057 (t) cc_final: 0.7773 (m) REVERT: B 826 VAL cc_start: 0.8967 (p) cc_final: 0.8685 (t) REVERT: B 850 ILE cc_start: 0.8006 (mp) cc_final: 0.7662 (mm) REVERT: B 1118 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: B 1125 ASN cc_start: 0.7888 (m-40) cc_final: 0.7538 (t0) REVERT: B 1138 TYR cc_start: 0.7835 (t80) cc_final: 0.7542 (t80) REVERT: C 281 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: C 505 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: C 561 PRO cc_start: 0.8398 (Cg_exo) cc_final: 0.8113 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8591 (t0) cc_final: 0.8388 (t0) REVERT: C 748 GLU cc_start: 0.7600 (tp30) cc_final: 0.7296 (tp30) outliers start: 64 outliers final: 32 residues processed: 222 average time/residue: 1.1012 time to fit residues: 291.3972 Evaluate side-chains 204 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 394 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25945 Z= 0.250 Angle : 0.612 20.325 35321 Z= 0.311 Chirality : 0.047 0.261 4200 Planarity : 0.004 0.063 4493 Dihedral : 6.635 58.271 4627 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.59 % Allowed : 12.75 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.93 (0.14), residues: 3100 helix: -0.49 (0.20), residues: 687 sheet: -0.04 (0.20), residues: 671 loop : -2.22 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.007 0.001 HIS B1064 PHE 0.019 0.001 PHE B 392 TYR 0.024 0.001 TYR B 904 ARG 0.007 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 177 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7343 (pp20) cc_final: 0.7027 (pp20) REVERT: A 417 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7375 (mtpt) REVERT: A 420 ASP cc_start: 0.7738 (m-30) cc_final: 0.7332 (m-30) REVERT: A 563 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.4872 (mp10) REVERT: A 580 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.5789 (mt0) REVERT: A 773 GLU cc_start: 0.7965 (tt0) cc_final: 0.7616 (tt0) REVERT: B 53 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: B 237 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7139 (mtm110) REVERT: B 396 TYR cc_start: 0.7378 (m-80) cc_final: 0.7119 (m-80) REVERT: B 613 GLN cc_start: 0.7519 (mt0) cc_final: 0.6883 (pt0) REVERT: B 635 VAL cc_start: 0.8126 (t) cc_final: 0.7858 (m) REVERT: B 826 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8654 (t) REVERT: B 850 ILE cc_start: 0.7960 (mp) cc_final: 0.7611 (mm) REVERT: B 1118 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7394 (t70) REVERT: B 1125 ASN cc_start: 0.7879 (m-40) cc_final: 0.7535 (t0) REVERT: B 1138 TYR cc_start: 0.7812 (t80) cc_final: 0.7553 (t80) REVERT: C 129 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5808 (mttt) REVERT: C 281 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: C 505 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: C 561 PRO cc_start: 0.8382 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8583 (t0) cc_final: 0.8373 (t0) REVERT: C 748 GLU cc_start: 0.7640 (tp30) cc_final: 0.7300 (tp30) REVERT: C 988 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7083 (tm-30) outliers start: 69 outliers final: 37 residues processed: 224 average time/residue: 1.1367 time to fit residues: 303.3006 Evaluate side-chains 211 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25945 Z= 0.280 Angle : 0.635 19.893 35321 Z= 0.322 Chirality : 0.049 0.281 4200 Planarity : 0.004 0.060 4493 Dihedral : 6.462 58.193 4627 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.59 % Allowed : 13.55 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.79 (0.14), residues: 3100 helix: -0.24 (0.20), residues: 682 sheet: 0.06 (0.21), residues: 659 loop : -2.18 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.008 0.001 HIS B1064 PHE 0.019 0.002 PHE A 592 TYR 0.022 0.001 TYR B 904 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 170 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7412 (mtpt) REVERT: A 420 ASP cc_start: 0.7728 (m-30) cc_final: 0.7319 (m-30) REVERT: A 462 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7492 (mppt) REVERT: A 563 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.4883 (mp10) REVERT: A 773 GLU cc_start: 0.7985 (tt0) cc_final: 0.7606 (tt0) REVERT: A 1086 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8230 (mppt) REVERT: B 53 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: B 396 TYR cc_start: 0.7362 (m-80) cc_final: 0.7116 (m-80) REVERT: B 613 GLN cc_start: 0.7570 (mt0) cc_final: 0.6865 (pt0) REVERT: B 635 VAL cc_start: 0.8120 (t) cc_final: 0.7854 (m) REVERT: B 826 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8682 (t) REVERT: B 850 ILE cc_start: 0.8002 (mp) cc_final: 0.7638 (mm) REVERT: B 1118 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7446 (t70) REVERT: B 1125 ASN cc_start: 0.7858 (m-40) cc_final: 0.7532 (t0) REVERT: B 1138 TYR cc_start: 0.7848 (t80) cc_final: 0.7546 (t80) REVERT: C 129 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5737 (mttt) REVERT: C 281 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: C 505 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: C 554 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: C 561 PRO cc_start: 0.8403 (Cg_exo) cc_final: 0.8114 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8590 (t0) cc_final: 0.8387 (t0) REVERT: C 748 GLU cc_start: 0.7636 (tp30) cc_final: 0.7285 (tp30) outliers start: 69 outliers final: 42 residues processed: 219 average time/residue: 1.1133 time to fit residues: 293.1702 Evaluate side-chains 215 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 301 optimal weight: 0.3980 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25945 Z= 0.254 Angle : 0.615 19.316 35321 Z= 0.312 Chirality : 0.048 0.268 4200 Planarity : 0.004 0.060 4493 Dihedral : 6.223 57.884 4627 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.88 % Allowed : 13.84 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.65 (0.14), residues: 3100 helix: 0.00 (0.20), residues: 677 sheet: 0.15 (0.21), residues: 652 loop : -2.14 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.007 0.001 HIS B1064 PHE 0.017 0.001 PHE A 592 TYR 0.024 0.001 TYR A 170 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 170 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7470 (mtpt) REVERT: A 420 ASP cc_start: 0.7724 (m-30) cc_final: 0.7315 (m-30) REVERT: A 462 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7411 (mppt) REVERT: A 563 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.4929 (mp10) REVERT: A 773 GLU cc_start: 0.7991 (tt0) cc_final: 0.7595 (tt0) REVERT: A 1086 LYS cc_start: 0.8481 (mmpt) cc_final: 0.8228 (mppt) REVERT: B 53 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: B 237 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7093 (mtm110) REVERT: B 396 TYR cc_start: 0.7363 (m-80) cc_final: 0.7103 (m-80) REVERT: B 613 GLN cc_start: 0.7580 (mt0) cc_final: 0.6898 (pt0) REVERT: B 635 VAL cc_start: 0.8157 (t) cc_final: 0.7880 (m) REVERT: B 826 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8684 (t) REVERT: B 850 ILE cc_start: 0.7958 (mp) cc_final: 0.7608 (mm) REVERT: B 1118 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7453 (t70) REVERT: B 1125 ASN cc_start: 0.7814 (m-40) cc_final: 0.7521 (t0) REVERT: B 1138 TYR cc_start: 0.7835 (t80) cc_final: 0.7560 (t80) REVERT: C 129 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5688 (mttt) REVERT: C 239 GLN cc_start: 0.8380 (pt0) cc_final: 0.7984 (pt0) REVERT: C 281 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: C 505 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.5810 (m-80) REVERT: C 554 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 603 ASN cc_start: 0.8586 (t0) cc_final: 0.8383 (t0) REVERT: C 748 GLU cc_start: 0.7657 (tp30) cc_final: 0.7306 (tp30) outliers start: 77 outliers final: 48 residues processed: 227 average time/residue: 1.1357 time to fit residues: 308.5323 Evaluate side-chains 225 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 167 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25945 Z= 0.147 Angle : 0.557 17.868 35321 Z= 0.282 Chirality : 0.045 0.263 4200 Planarity : 0.004 0.059 4493 Dihedral : 5.759 57.116 4627 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.55 % Allowed : 14.38 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.35 (0.15), residues: 3100 helix: 0.39 (0.21), residues: 675 sheet: 0.34 (0.21), residues: 662 loop : -2.02 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.003 0.000 HIS B1064 PHE 0.017 0.001 PHE C 32 TYR 0.023 0.001 TYR A 170 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 183 time to evaluate : 3.004 Fit side-chains revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.5040 (tt) REVERT: A 417 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7433 (mmtt) REVERT: A 420 ASP cc_start: 0.7754 (m-30) cc_final: 0.7364 (m-30) REVERT: A 462 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7345 (mppt) REVERT: A 563 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.4908 (mp10) REVERT: A 773 GLU cc_start: 0.7919 (tt0) cc_final: 0.7560 (tt0) REVERT: A 1125 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7804 (m110) REVERT: B 53 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: B 237 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7119 (mtm110) REVERT: B 396 TYR cc_start: 0.7341 (m-80) cc_final: 0.7070 (m-80) REVERT: B 613 GLN cc_start: 0.7486 (mt0) cc_final: 0.6888 (pt0) REVERT: B 635 VAL cc_start: 0.8188 (t) cc_final: 0.7983 (m) REVERT: B 826 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8630 (t) REVERT: B 850 ILE cc_start: 0.7928 (mp) cc_final: 0.7586 (mm) REVERT: B 1125 ASN cc_start: 0.7797 (m-40) cc_final: 0.7492 (t0) REVERT: B 1138 TYR cc_start: 0.7858 (t80) cc_final: 0.7577 (t80) REVERT: C 129 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5680 (mttt) REVERT: C 202 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8087 (mmtp) REVERT: C 205 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8785 (t) REVERT: C 239 GLN cc_start: 0.8345 (pt0) cc_final: 0.7891 (pt0) REVERT: C 271 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7117 (mt0) REVERT: C 281 GLU cc_start: 0.7931 (pt0) cc_final: 0.7589 (pm20) REVERT: C 505 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: C 554 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: C 561 PRO cc_start: 0.8403 (Cg_exo) cc_final: 0.8138 (Cg_endo) REVERT: C 748 GLU cc_start: 0.7635 (tp30) cc_final: 0.7296 (tp30) outliers start: 68 outliers final: 37 residues processed: 231 average time/residue: 1.1637 time to fit residues: 320.8737 Evaluate side-chains 219 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 169 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 0.0060 chunk 236 optimal weight: 4.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25945 Z= 0.198 Angle : 0.577 17.676 35321 Z= 0.293 Chirality : 0.046 0.255 4200 Planarity : 0.004 0.059 4493 Dihedral : 5.692 57.008 4627 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.73 % Allowed : 14.82 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.29 (0.15), residues: 3100 helix: 0.47 (0.21), residues: 675 sheet: 0.34 (0.21), residues: 662 loop : -1.97 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.001 PHE A 855 TYR 0.019 0.001 TYR C1067 ARG 0.012 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 170 time to evaluate : 2.997 Fit side-chains revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4949 (tt) REVERT: A 420 ASP cc_start: 0.7755 (m-30) cc_final: 0.7338 (m-30) REVERT: A 563 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.4902 (mp10) REVERT: A 580 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.5647 (mt0) REVERT: A 773 GLU cc_start: 0.7947 (tt0) cc_final: 0.7573 (tt0) REVERT: A 868 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: A 1125 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7857 (m110) REVERT: B 53 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.7013 (m-30) REVERT: B 237 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7117 (mtm110) REVERT: B 396 TYR cc_start: 0.7341 (m-80) cc_final: 0.7064 (m-80) REVERT: B 613 GLN cc_start: 0.7558 (mt0) cc_final: 0.6880 (pt0) REVERT: B 635 VAL cc_start: 0.8212 (t) cc_final: 0.7992 (m) REVERT: B 826 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8644 (t) REVERT: B 850 ILE cc_start: 0.7940 (mp) cc_final: 0.7587 (mm) REVERT: B 1125 ASN cc_start: 0.7793 (m-40) cc_final: 0.7491 (t0) REVERT: B 1138 TYR cc_start: 0.7858 (t80) cc_final: 0.7565 (t80) REVERT: C 102 ARG cc_start: 0.6662 (mmt90) cc_final: 0.4942 (mtp180) REVERT: C 129 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.5653 (mttt) REVERT: C 202 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8064 (mmtp) REVERT: C 205 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8796 (t) REVERT: C 239 GLN cc_start: 0.8368 (pt0) cc_final: 0.7953 (pt0) REVERT: C 271 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: C 281 GLU cc_start: 0.7918 (pt0) cc_final: 0.7571 (pm20) REVERT: C 465 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: C 505 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: C 748 GLU cc_start: 0.7666 (tp30) cc_final: 0.7329 (tp30) outliers start: 73 outliers final: 42 residues processed: 223 average time/residue: 1.1772 time to fit residues: 311.0523 Evaluate side-chains 221 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.1980 chunk 288 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 279 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25945 Z= 0.146 Angle : 0.544 16.621 35321 Z= 0.276 Chirality : 0.045 0.252 4200 Planarity : 0.004 0.061 4493 Dihedral : 5.389 56.827 4627 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.26 % Allowed : 15.59 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.11 (0.15), residues: 3100 helix: 0.68 (0.21), residues: 678 sheet: 0.46 (0.21), residues: 650 loop : -1.88 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.003 0.000 HIS B1064 PHE 0.017 0.001 PHE A 133 TYR 0.024 0.001 TYR A 170 ARG 0.014 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 173 time to evaluate : 2.838 Fit side-chains revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4986 (tt) REVERT: A 420 ASP cc_start: 0.7738 (m-30) cc_final: 0.7331 (m-30) REVERT: A 563 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.4918 (mp10) REVERT: A 580 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5607 (mt0) REVERT: A 773 GLU cc_start: 0.7909 (tt0) cc_final: 0.7563 (tt0) REVERT: A 868 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: A 1002 GLN cc_start: 0.7890 (tt0) cc_final: 0.7427 (mt0) REVERT: B 53 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: B 396 TYR cc_start: 0.7331 (m-80) cc_final: 0.7055 (m-80) REVERT: B 613 GLN cc_start: 0.7547 (mt0) cc_final: 0.6835 (pt0) REVERT: B 826 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8569 (t) REVERT: B 850 ILE cc_start: 0.7861 (mp) cc_final: 0.7534 (mm) REVERT: B 1125 ASN cc_start: 0.7753 (m-40) cc_final: 0.7401 (t0) REVERT: B 1138 TYR cc_start: 0.7807 (t80) cc_final: 0.7514 (t80) REVERT: C 129 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5643 (mttt) REVERT: C 202 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8013 (mmtp) REVERT: C 271 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: C 281 GLU cc_start: 0.7910 (pt0) cc_final: 0.7699 (pm20) REVERT: C 324 GLU cc_start: 0.8151 (pm20) cc_final: 0.7446 (pm20) REVERT: C 465 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: C 505 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: C 561 PRO cc_start: 0.8375 (Cg_exo) cc_final: 0.8104 (Cg_endo) REVERT: C 619 GLU cc_start: 0.7359 (pt0) cc_final: 0.7121 (pt0) REVERT: C 748 GLU cc_start: 0.7658 (tp30) cc_final: 0.7337 (tp30) outliers start: 60 outliers final: 39 residues processed: 218 average time/residue: 1.1191 time to fit residues: 291.2134 Evaluate side-chains 212 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 0.2980 chunk 180 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 675 GLN C 314 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25945 Z= 0.146 Angle : 0.539 15.680 35321 Z= 0.273 Chirality : 0.045 0.252 4200 Planarity : 0.004 0.063 4493 Dihedral : 5.254 56.874 4627 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.18 % Allowed : 15.80 % Favored : 82.01 % 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: -0.95 (0.15), residues: 3100 helix: 0.79 (0.21), residues: 686 sheet: 0.51 (0.21), residues: 651 loop : -1.75 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.003 0.000 HIS B1064 PHE 0.016 0.001 PHE C 32 TYR 0.023 0.001 TYR B 904 ARG 0.014 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 171 time to evaluate : 2.694 Fit side-chains revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5144 (OUTLIER) cc_final: 0.4895 (tt) REVERT: A 402 ILE cc_start: 0.6879 (pt) cc_final: 0.6670 (pt) REVERT: A 420 ASP cc_start: 0.7715 (m-30) cc_final: 0.7334 (m-30) REVERT: A 563 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.4907 (mp10) REVERT: A 580 GLN cc_start: 0.5855 (OUTLIER) cc_final: 0.5610 (mt0) REVERT: A 646 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7734 (mtp180) REVERT: A 773 GLU cc_start: 0.7903 (tt0) cc_final: 0.7552 (tt0) REVERT: A 787 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: A 868 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: A 1002 GLN cc_start: 0.7879 (tt0) cc_final: 0.7427 (mt0) REVERT: B 53 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: B 396 TYR cc_start: 0.7343 (m-80) cc_final: 0.7086 (m-80) REVERT: B 613 GLN cc_start: 0.7560 (mt0) cc_final: 0.6837 (pt0) REVERT: B 826 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8564 (t) REVERT: B 850 ILE cc_start: 0.7843 (mp) cc_final: 0.7526 (mm) REVERT: B 1125 ASN cc_start: 0.7713 (m-40) cc_final: 0.7356 (t0) REVERT: B 1138 TYR cc_start: 0.7789 (t80) cc_final: 0.7517 (t80) REVERT: C 129 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.5667 (mttt) REVERT: C 202 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7984 (mmtp) REVERT: C 271 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: C 281 GLU cc_start: 0.7994 (pt0) cc_final: 0.7694 (pm20) REVERT: C 324 GLU cc_start: 0.8168 (pm20) cc_final: 0.7478 (pm20) REVERT: C 465 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: C 505 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: C 561 PRO cc_start: 0.8364 (Cg_exo) cc_final: 0.8089 (Cg_endo) REVERT: C 748 GLU cc_start: 0.7672 (tp30) cc_final: 0.7345 (tp30) outliers start: 58 outliers final: 37 residues processed: 213 average time/residue: 1.2227 time to fit residues: 310.6047 Evaluate side-chains 207 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 158 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 4.9990 chunk 263 optimal weight: 0.0070 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1101 HIS B 30 ASN B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 564 GLN C 613 GLN C1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111604 restraints weight = 42323.974| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.92 r_work: 0.3034 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25945 Z= 0.163 Angle : 0.546 15.648 35321 Z= 0.278 Chirality : 0.045 0.251 4200 Planarity : 0.004 0.065 4493 Dihedral : 5.257 56.761 4627 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.15 % Allowed : 15.99 % Favored : 81.86 % 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: -0.93 (0.15), residues: 3100 helix: 0.79 (0.21), residues: 686 sheet: 0.51 (0.21), residues: 660 loop : -1.73 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS B1064 PHE 0.018 0.001 PHE A 133 TYR 0.027 0.001 TYR A 170 ARG 0.014 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7452.89 seconds wall clock time: 135 minutes 21.43 seconds (8121.43 seconds total)