Starting phenix.real_space_refine on Fri Aug 9 09:19:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm5_22256/08_2024/6xm5_22256.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm5_22256/08_2024/6xm5_22256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm5_22256/08_2024/6xm5_22256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm5_22256/08_2024/6xm5_22256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm5_22256/08_2024/6xm5_22256.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm5_22256/08_2024/6xm5_22256.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 16154 2.51 5 N 4148 2.21 5 O 4981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A ARG 847": "NH1" <-> "NH2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "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 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "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 GLU 661": "OE1" <-> "OE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1107": "NH1" <-> "NH2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25393 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8249 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 6 Chain: "B" Number of atoms: 8242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8242 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "C" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8090 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 983} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: "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: 13.58, per 1000 atoms: 0.53 Number of scatterers: 25393 At special positions: 0 Unit cell: (142.8, 138.55, 180.2, 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 4981 8.00 N 4148 7.00 C 16154 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.02 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-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 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " Time building additional restraints: 8.85 Conformation dependent library (CDL) restraints added in 4.5 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.546A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.018A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 634 through 638 removed outlier: 4.048A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.646A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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: 3.773A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.639A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.328A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.704A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.126A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.517A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.658A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.587A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.574A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.659A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.322A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.533A 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 337 through 343 removed outlier: 4.403A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.750A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.239A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.549A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.567A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.719A 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 760 through 783 removed outlier: 4.115A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 839 removed outlier: 3.524A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.527A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.782A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.521A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.747A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.837A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.528A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.500A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.721A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 990 removed outlier: 4.347A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1016 Processing helix chain 'B' and resid 1017 through 1033 removed outlier: 3.735A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.990A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.593A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.949A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.510A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.507A pdb=" N TRP C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.789A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.736A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.507A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 885 removed outlier: 3.572A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.040A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.701A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.815A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.758A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.849A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 993 removed outlier: 4.050A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1032 removed outlier: 3.663A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.759A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.472A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.491A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.534A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.639A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.549A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.609A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.861A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.838A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.838A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.684A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.439A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.930A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.623A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.822A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.536A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.819A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.670A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.515A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.514A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.925A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.984A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.577A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.539A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.746A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.565A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 115 through 119 Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.621A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.173A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.706A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 539 through 540 removed outlier: 5.339A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.819A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.755A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 784 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8061 1.35 - 1.48: 6922 1.48 - 1.61: 10836 1.61 - 1.74: 1 1.74 - 1.87: 133 Bond restraints: 25953 Sorted by residual: bond pdb=" C LYS A 790 " pdb=" N THR A 791 " ideal model delta sigma weight residual 1.331 1.258 0.073 2.07e-02 2.33e+03 1.23e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 25948 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.79: 533 105.79 - 112.93: 13952 112.93 - 120.07: 9191 120.07 - 127.21: 11439 127.21 - 134.35: 215 Bond angle restraints: 35330 Sorted by residual: angle pdb=" C PHE A 392 " pdb=" N THR A 393 " pdb=" CA THR A 393 " ideal model delta sigma weight residual 121.54 132.67 -11.13 1.91e+00 2.74e-01 3.39e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.25 -5.55 1.22e+00 6.72e-01 2.07e+01 angle pdb=" N GLU B1144 " pdb=" CA GLU B1144 " pdb=" C GLU B1144 " ideal model delta sigma weight residual 114.56 109.09 5.47 1.27e+00 6.20e-01 1.85e+01 ... (remaining 35325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14409 17.82 - 35.64: 1429 35.64 - 53.45: 304 53.45 - 71.27: 53 71.27 - 89.09: 19 Dihedral angle restraints: 16214 sinusoidal: 7039 harmonic: 9175 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 171.03 -78.03 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 163.21 -70.21 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -16.23 -69.77 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 16211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3395 0.073 - 0.147: 728 0.147 - 0.220: 65 0.220 - 0.293: 5 0.293 - 0.367: 3 Chirality restraints: 4196 Sorted by residual: chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR C 33 " pdb=" CA THR C 33 " pdb=" OG1 THR C 33 " pdb=" CG2 THR C 33 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.62e+00 ... (remaining 4193 not shown) Planarity restraints: 4539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 987 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO B 987 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.059 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO C 987 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.049 5.00e-02 4.00e+02 ... (remaining 4536 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6893 2.80 - 3.32: 20417 3.32 - 3.85: 39812 3.85 - 4.37: 44770 4.37 - 4.90: 81320 Nonbonded interactions: 193212 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR C 676 " pdb=" OE1 GLN C 690 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.294 3.040 ... (remaining 193207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 828 or (resid 850 and (name N or name CA or name C or name O or name CB )) or \ resid 851 through 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 828 or (resid 850 and \ (name N or name CA or name C or name O or name CB )) or resid 851 through 1147 o \ r resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 1147 or resid 1301 thr \ ough 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.280 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: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 66.010 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.008 0.091 25953 Z= 0.515 Angle : 0.856 11.970 35330 Z= 0.457 Chirality : 0.059 0.367 4196 Planarity : 0.007 0.115 4497 Dihedral : 14.526 89.088 10183 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.51 % Allowed : 8.88 % Favored : 90.61 % 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: -4.06 (0.12), residues: 3105 helix: -2.87 (0.15), residues: 641 sheet: -1.53 (0.19), residues: 651 loop : -3.22 (0.11), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS A1064 PHE 0.049 0.002 PHE B 906 TYR 0.031 0.002 TYR C 453 ARG 0.004 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 229 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8288 (t80) cc_final: 0.8031 (t80) REVERT: A 351 TYR cc_start: 0.8261 (p90) cc_final: 0.7806 (p90) REVERT: A 452 LEU cc_start: 0.8429 (tp) cc_final: 0.8144 (tp) REVERT: A 540 ASN cc_start: 0.7949 (m110) cc_final: 0.7702 (m110) REVERT: B 201 PHE cc_start: 0.7841 (t80) cc_final: 0.7611 (t80) REVERT: B 266 TYR cc_start: 0.5569 (m-80) cc_final: 0.5272 (m-80) REVERT: B 375 SER cc_start: 0.7665 (p) cc_final: 0.7392 (p) REVERT: C 238 PHE cc_start: 0.6192 (p90) cc_final: 0.5562 (p90) outliers start: 14 outliers final: 5 residues processed: 242 average time/residue: 0.3310 time to fit residues: 131.6749 Evaluate side-chains 176 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 294 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 264 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 182 optimal weight: 0.7980 chunk 284 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 354 ASN A 360 ASN A 613 GLN A 710 ASN A 935 GLN B 81 ASN B 334 ASN B 487 ASN B 519 HIS B 764 ASN B 901 GLN B 957 GLN B 965 GLN C 196 ASN C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 901 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25953 Z= 0.196 Angle : 0.569 9.703 35330 Z= 0.299 Chirality : 0.045 0.245 4196 Planarity : 0.005 0.093 4497 Dihedral : 7.174 59.473 4597 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.27 % Allowed : 11.24 % Favored : 87.48 % 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: -2.95 (0.13), residues: 3105 helix: -1.09 (0.19), residues: 628 sheet: -1.05 (0.19), residues: 689 loop : -2.79 (0.12), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.025 0.001 PHE C 92 TYR 0.021 0.001 TYR A1067 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7753 (tp) cc_final: 0.7361 (tp) REVERT: A 170 TYR cc_start: 0.7909 (t80) cc_final: 0.7708 (t80) REVERT: A 351 TYR cc_start: 0.8258 (p90) cc_final: 0.7968 (p90) REVERT: B 201 PHE cc_start: 0.7887 (t80) cc_final: 0.7675 (t80) REVERT: B 266 TYR cc_start: 0.5568 (m-80) cc_final: 0.5218 (m-80) REVERT: B 338 PHE cc_start: 0.8013 (m-10) cc_final: 0.7516 (m-80) REVERT: B 353 TRP cc_start: 0.8069 (p-90) cc_final: 0.7766 (p-90) REVERT: B 365 TYR cc_start: 0.8311 (m-80) cc_final: 0.8030 (m-80) REVERT: C 238 PHE cc_start: 0.6191 (p90) cc_final: 0.5604 (p90) REVERT: C 867 ASP cc_start: 0.7028 (t0) cc_final: 0.6804 (t0) outliers start: 35 outliers final: 19 residues processed: 221 average time/residue: 0.3757 time to fit residues: 136.3163 Evaluate side-chains 191 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 157 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 282 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25953 Z= 0.275 Angle : 0.568 9.583 35330 Z= 0.296 Chirality : 0.045 0.240 4196 Planarity : 0.005 0.063 4497 Dihedral : 6.628 58.141 4593 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.04 % Allowed : 12.52 % Favored : 85.44 % 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: -2.55 (0.14), residues: 3105 helix: -0.55 (0.20), residues: 638 sheet: -0.83 (0.19), residues: 682 loop : -2.60 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 PHE 0.039 0.001 PHE A 562 TYR 0.021 0.001 TYR A1067 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 187 time to evaluate : 2.917 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7749 (tp) cc_final: 0.7301 (tp) REVERT: A 170 TYR cc_start: 0.7967 (t80) cc_final: 0.7706 (t80) REVERT: A 351 TYR cc_start: 0.8247 (p90) cc_final: 0.7779 (p90) REVERT: A 525 CYS cc_start: 0.4566 (OUTLIER) cc_final: 0.3875 (m) REVERT: A 878 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9003 (tt) REVERT: B 140 PHE cc_start: 0.5641 (p90) cc_final: 0.5348 (p90) REVERT: B 266 TYR cc_start: 0.5515 (m-80) cc_final: 0.5170 (m-80) REVERT: B 353 TRP cc_start: 0.8072 (p-90) cc_final: 0.7741 (p-90) REVERT: B 365 TYR cc_start: 0.8314 (m-80) cc_final: 0.8073 (m-80) REVERT: B 508 TYR cc_start: 0.8224 (m-80) cc_final: 0.7897 (m-80) REVERT: C 238 PHE cc_start: 0.6183 (p90) cc_final: 0.5854 (p90) outliers start: 56 outliers final: 30 residues processed: 237 average time/residue: 0.3250 time to fit residues: 129.9104 Evaluate side-chains 206 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 281 optimal weight: 0.6980 chunk 214 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 191 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25953 Z= 0.212 Angle : 0.533 9.509 35330 Z= 0.277 Chirality : 0.045 0.233 4196 Planarity : 0.004 0.063 4497 Dihedral : 6.030 57.239 4593 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.22 % Allowed : 13.68 % Favored : 84.10 % 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: -2.17 (0.14), residues: 3105 helix: -0.01 (0.21), residues: 634 sheet: -0.67 (0.19), residues: 693 loop : -2.41 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 PHE 0.026 0.001 PHE C 92 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7080 (m-40) cc_final: 0.6336 (t0) REVERT: A 170 TYR cc_start: 0.7954 (t80) cc_final: 0.7670 (t80) REVERT: A 351 TYR cc_start: 0.8228 (p90) cc_final: 0.7692 (p90) REVERT: A 533 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4144 (mp) REVERT: A 878 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8997 (tt) REVERT: B 140 PHE cc_start: 0.5602 (p90) cc_final: 0.5232 (p90) REVERT: B 212 LEU cc_start: 0.3641 (OUTLIER) cc_final: 0.2905 (mm) REVERT: B 266 TYR cc_start: 0.5524 (m-80) cc_final: 0.5175 (m-80) REVERT: B 353 TRP cc_start: 0.8072 (p-90) cc_final: 0.7807 (p-90) REVERT: B 365 TYR cc_start: 0.8321 (m-80) cc_final: 0.8054 (m-80) REVERT: B 508 TYR cc_start: 0.8185 (m-80) cc_final: 0.7488 (m-80) REVERT: C 237 ARG cc_start: 0.7258 (mmt180) cc_final: 0.6662 (ptm-80) outliers start: 61 outliers final: 33 residues processed: 247 average time/residue: 0.3771 time to fit residues: 155.6394 Evaluate side-chains 217 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 251 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 225 optimal weight: 0.0060 chunk 124 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25953 Z= 0.298 Angle : 0.565 9.802 35330 Z= 0.293 Chirality : 0.046 0.233 4196 Planarity : 0.004 0.063 4497 Dihedral : 5.974 57.212 4592 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.77 % Allowed : 13.61 % Favored : 83.62 % 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: -2.08 (0.14), residues: 3105 helix: 0.09 (0.21), residues: 638 sheet: -0.58 (0.19), residues: 691 loop : -2.39 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.006 0.001 HIS A1064 PHE 0.028 0.001 PHE C 92 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7956 (t80) cc_final: 0.7666 (t80) REVERT: A 351 TYR cc_start: 0.8248 (p90) cc_final: 0.7697 (p90) REVERT: A 533 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4254 (mp) REVERT: A 878 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9015 (tt) REVERT: B 140 PHE cc_start: 0.5542 (p90) cc_final: 0.5188 (p90) REVERT: B 212 LEU cc_start: 0.3536 (OUTLIER) cc_final: 0.2840 (mm) REVERT: B 239 GLN cc_start: 0.5982 (tm-30) cc_final: 0.5198 (tm-30) REVERT: B 266 TYR cc_start: 0.5474 (m-80) cc_final: 0.5129 (m-80) REVERT: B 353 TRP cc_start: 0.8061 (p-90) cc_final: 0.7809 (p-90) REVERT: B 357 ARG cc_start: 0.6007 (tpp80) cc_final: 0.5661 (tpp80) REVERT: B 365 TYR cc_start: 0.8340 (m-80) cc_final: 0.8114 (m-80) REVERT: B 508 TYR cc_start: 0.8248 (m-80) cc_final: 0.7488 (m-80) REVERT: C 237 ARG cc_start: 0.7149 (mmt180) cc_final: 0.6593 (ptm-80) REVERT: C 505 TYR cc_start: 0.8034 (m-80) cc_final: 0.7824 (m-80) REVERT: C 697 MET cc_start: 0.8678 (ptm) cc_final: 0.8440 (ptm) outliers start: 76 outliers final: 57 residues processed: 257 average time/residue: 0.3183 time to fit residues: 136.7616 Evaluate side-chains 242 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 182 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 25 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25953 Z= 0.214 Angle : 0.531 9.624 35330 Z= 0.275 Chirality : 0.045 0.231 4196 Planarity : 0.004 0.061 4497 Dihedral : 5.689 56.521 4592 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.47 % Allowed : 14.77 % Favored : 82.75 % 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: -1.85 (0.14), residues: 3105 helix: 0.41 (0.21), residues: 635 sheet: -0.47 (0.19), residues: 695 loop : -2.28 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.022 0.001 PHE C 92 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 190 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7938 (t80) cc_final: 0.7651 (t80) REVERT: A 249 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.4877 (mp) REVERT: A 351 TYR cc_start: 0.8227 (p90) cc_final: 0.7640 (p90) REVERT: A 533 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4298 (mp) REVERT: A 878 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (tt) REVERT: B 140 PHE cc_start: 0.5457 (p90) cc_final: 0.5131 (p90) REVERT: B 212 LEU cc_start: 0.3332 (OUTLIER) cc_final: 0.2714 (mm) REVERT: B 266 TYR cc_start: 0.5486 (m-80) cc_final: 0.5135 (m-80) REVERT: B 353 TRP cc_start: 0.8065 (p-90) cc_final: 0.7839 (p-90) REVERT: B 357 ARG cc_start: 0.6262 (tpp80) cc_final: 0.5808 (tpp80) REVERT: B 365 TYR cc_start: 0.8352 (m-80) cc_final: 0.8087 (m-80) REVERT: B 508 TYR cc_start: 0.8277 (m-80) cc_final: 0.7299 (m-80) REVERT: C 237 ARG cc_start: 0.7149 (mmt180) cc_final: 0.6570 (ptm-80) REVERT: C 474 GLN cc_start: 0.7098 (pp30) cc_final: 0.6620 (pp30) REVERT: C 697 MET cc_start: 0.8674 (ptm) cc_final: 0.8458 (ptm) outliers start: 68 outliers final: 49 residues processed: 248 average time/residue: 0.2809 time to fit residues: 115.2325 Evaluate side-chains 233 residues out of total 2749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 221 optimal weight: 0.0170 chunk 171 optimal weight: 0.0000 chunk 254 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 301 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 overall best weight: 0.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: