Starting phenix.real_space_refine on Fri Aug 9 10:50:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whw_37550/08_2024/8whw_37550.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whw_37550/08_2024/8whw_37550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whw_37550/08_2024/8whw_37550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whw_37550/08_2024/8whw_37550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whw_37550/08_2024/8whw_37550.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whw_37550/08_2024/8whw_37550.cif" } resolution = 3.85 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= 0.002 sd= 0.058 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 114 5.16 5 C 16452 2.51 5 N 4197 2.21 5 O 5044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C PHE 939": "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 1017": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25807 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" 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 Time building chain proxies: 13.78, per 1000 atoms: 0.53 Number of scatterers: 25807 At special positions: 0 Unit cell: (147, 135, 189, 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 114 16.00 O 5044 8.00 N 4197 7.00 C 16452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 354 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 331 " " NAG D 1 " - " ASN A 354 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 282 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN C 354 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1098 " Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 4.4 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 53 sheets defined 25.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.547A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.831A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.793A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.581A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.283A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.602A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.161A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.848A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.502A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.906A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.691A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.680A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.901A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.641A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.733A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.203A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.666A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.581A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.802A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.395A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.654A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.729A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.874A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.550A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 627 removed outlier: 3.568A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.573A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.612A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.310A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.694A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.726A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.146A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.797A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.681A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.573A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.879A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.850A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.814A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.713A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.296A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 removed outlier: 4.059A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 7.254A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 3.759A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.086A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.605A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.524A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.167A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.355A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.946A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.078A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.723A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.372A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.154A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.913A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.948A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.624A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.014A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.403A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.790A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.222A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.818A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.685A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.313A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.732A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.184A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.084A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.506A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 909 hydrogen bonds defined for protein. 2490 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: 10.81 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4837 1.33 - 1.45: 7048 1.45 - 1.58: 14380 1.58 - 1.70: 1 1.70 - 1.83: 141 Bond restraints: 26407 Sorted by residual: bond pdb=" CA PHE C 216 " pdb=" C PHE C 216 " ideal model delta sigma weight residual 1.534 1.490 0.044 9.50e-03 1.11e+04 2.12e+01 bond pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" CA HIS B 207 " pdb=" C HIS B 207 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.25e-02 6.40e+03 1.72e+01 bond pdb=" CA THR B 208 " pdb=" C THR B 208 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.26e-02 6.30e+03 1.27e+01 ... (remaining 26402 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.19: 203 103.19 - 110.98: 9993 110.98 - 118.76: 11418 118.76 - 126.54: 14035 126.54 - 134.33: 291 Bond angle restraints: 35940 Sorted by residual: angle pdb=" C GLN A 218 " pdb=" N GLY A 219 " pdb=" CA GLY A 219 " ideal model delta sigma weight residual 120.10 113.74 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N GLY B 213 " pdb=" CA GLY B 213 " pdb=" C GLY B 213 " ideal model delta sigma weight residual 115.21 106.68 8.53 1.30e+00 5.92e-01 4.30e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.66 -7.96 1.22e+00 6.72e-01 4.25e+01 angle pdb=" N PRO B 209 " pdb=" CA PRO B 209 " pdb=" C PRO B 209 " ideal model delta sigma weight residual 112.47 99.14 13.33 2.06e+00 2.36e-01 4.19e+01 angle pdb=" N VAL C 570 " pdb=" CA VAL C 570 " pdb=" C VAL C 570 " ideal model delta sigma weight residual 106.21 112.30 -6.09 1.07e+00 8.73e-01 3.24e+01 ... (remaining 35935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 14728 23.11 - 46.21: 1382 46.21 - 69.32: 171 69.32 - 92.42: 139 92.42 - 115.53: 118 Dihedral angle restraints: 16538 sinusoidal: 7262 harmonic: 9276 Sorted by residual: dihedral pdb=" CD ARG C 328 " pdb=" NE ARG C 328 " pdb=" CZ ARG C 328 " pdb=" NH1 ARG C 328 " ideal model delta sinusoidal sigma weight residual 0.00 -64.56 64.56 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 39.96 53.04 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 142.22 -49.22 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 16535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4184 0.182 - 0.364: 58 0.364 - 0.547: 3 0.547 - 0.729: 0 0.729 - 0.911: 3 Chirality restraints: 4248 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 4245 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.251 2.00e-02 2.50e+03 2.09e-01 5.44e+02 pdb=" C7 NAG C1303 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.345 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.240 2.00e-02 2.50e+03 2.06e-01 5.30e+02 pdb=" C7 NAG B1303 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.345 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.212 2.00e-02 2.50e+03 1.78e-01 3.96e+02 pdb=" C7 NAG C1301 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.006 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 911 2.68 - 3.24: 26089 3.24 - 3.79: 41366 3.79 - 4.35: 53807 4.35 - 4.90: 87967 Nonbonded interactions: 210140 Sorted by model distance: nonbonded pdb=" O PRO C 486 " pdb=" ND2 ASN C 487 " model vdw 2.128 3.120 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.183 3.120 nonbonded pdb=" O ASN C 417 " pdb=" ND2 ASN C 422 " model vdw 2.195 3.120 nonbonded pdb=" CG2 ILE B 210 " pdb=" N ILE B 212 " model vdw 2.199 3.540 nonbonded pdb=" OG1 THR C 393 " pdb=" OE1 GLU C 516 " model vdw 2.202 3.040 ... (remaining 210135 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' selection = (chain 'B' and (resid 23 through 1144 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 68.810 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.150 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 26407 Z= 0.405 Angle : 0.947 13.332 35940 Z= 0.558 Chirality : 0.065 0.911 4248 Planarity : 0.012 0.444 4557 Dihedral : 21.278 115.525 10463 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.80 % Favored : 90.63 % Rotamer: Outliers : 1.91 % Allowed : 24.00 % Favored : 74.09 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3159 helix: 0.49 (0.20), residues: 716 sheet: -1.28 (0.21), residues: 598 loop : -2.18 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.022 0.002 PHE C 338 TYR 0.022 0.002 TYR B 501 ARG 0.020 0.001 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6394 (mmp) cc_final: 0.5799 (mmp) REVERT: A 591 SER cc_start: 0.7715 (t) cc_final: 0.7320 (p) REVERT: A 896 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (mt) REVERT: B 270 LEU cc_start: 0.9136 (mp) cc_final: 0.8627 (mp) REVERT: B 568 ASP cc_start: 0.6673 (t0) cc_final: 0.6455 (t0) REVERT: B 619 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8081 (tm-30) REVERT: B 740 MET cc_start: 0.8058 (ttm) cc_final: 0.7767 (ttm) REVERT: B 773 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6537 (tm-30) REVERT: B 850 ILE cc_start: 0.7890 (mm) cc_final: 0.7459 (mm) REVERT: C 303 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 327 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9124 (t) REVERT: C 453 TYR cc_start: 0.7355 (p90) cc_final: 0.7128 (p90) outliers start: 53 outliers final: 17 residues processed: 236 average time/residue: 0.3607 time to fit residues: 138.4746 Evaluate side-chains 172 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 804 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26407 Z= 0.269 Angle : 0.745 13.018 35940 Z= 0.369 Chirality : 0.052 0.620 4248 Planarity : 0.005 0.063 4557 Dihedral : 14.534 111.907 4785 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.76 % Favored : 92.12 % Rotamer: Outliers : 4.32 % Allowed : 21.80 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3159 helix: 0.96 (0.20), residues: 706 sheet: -1.21 (0.20), residues: 625 loop : -2.01 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 633 HIS 0.003 0.001 HIS C 339 PHE 0.025 0.002 PHE B 216 TYR 0.022 0.001 TYR B 501 ARG 0.007 0.001 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 179 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8886 (tptm) REVERT: A 630 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8200 (m) REVERT: B 84 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7063 (mm) REVERT: B 104 TRP cc_start: 0.6456 (m-10) cc_final: 0.6182 (m-10) REVERT: B 164 ASN cc_start: 0.3660 (OUTLIER) cc_final: 0.3330 (p0) REVERT: B 270 LEU cc_start: 0.9164 (mp) cc_final: 0.8857 (mp) REVERT: B 304 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9105 (mtmt) REVERT: B 734 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8805 (p) REVERT: B 740 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7950 (ttm) REVERT: B 773 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7018 (tm-30) REVERT: B 850 ILE cc_start: 0.7887 (mm) cc_final: 0.7471 (mm) REVERT: B 873 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8095 (t80) REVERT: C 303 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9111 (pp) REVERT: C 1037 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8972 (t) outliers start: 120 outliers final: 45 residues processed: 289 average time/residue: 0.3346 time to fit residues: 162.5022 Evaluate side-chains 197 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 142 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1036 GLN A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26407 Z= 0.212 Angle : 0.675 10.008 35940 Z= 0.337 Chirality : 0.052 0.720 4248 Planarity : 0.005 0.067 4557 Dihedral : 10.421 110.717 4771 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 3.86 % Allowed : 22.49 % Favored : 73.66 % 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: -1.58 (0.14), residues: 3159 helix: 1.11 (0.20), residues: 710 sheet: -1.32 (0.20), residues: 599 loop : -1.91 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.004 0.001 HIS A 339 PHE 0.027 0.001 PHE B 92 TYR 0.020 0.001 TYR B 501 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 161 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: A 714 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8928 (pt) REVERT: A 816 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8380 (m) REVERT: B 84 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7191 (mm) REVERT: B 270 LEU cc_start: 0.9178 (mp) cc_final: 0.8937 (mp) REVERT: B 613 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: B 698 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 740 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7931 (ttm) REVERT: B 773 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6821 (tm-30) REVERT: B 850 ILE cc_start: 0.7931 (mm) cc_final: 0.7536 (mm) REVERT: B 869 MET cc_start: 0.8695 (ptt) cc_final: 0.8397 (ptt) REVERT: B 873 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 1037 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8937 (t) outliers start: 107 outliers final: 62 residues processed: 256 average time/residue: 0.3298 time to fit residues: 141.9247 Evaluate side-chains 214 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 143 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 2.9990 chunk 217 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26407 Z= 0.225 Angle : 0.642 9.110 35940 Z= 0.323 Chirality : 0.049 0.599 4248 Planarity : 0.004 0.071 4557 Dihedral : 8.657 103.901 4767 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 3.96 % Allowed : 22.81 % Favored : 73.23 % 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: -1.45 (0.14), residues: 3159 helix: 1.21 (0.20), residues: 704 sheet: -1.06 (0.20), residues: 622 loop : -1.89 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 104 HIS 0.003 0.001 HIS A 339 PHE 0.029 0.001 PHE C 133 TYR 0.019 0.001 TYR B 501 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 165 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8209 (tpp80) REVERT: A 456 PHE cc_start: 0.7815 (m-80) cc_final: 0.7353 (m-80) REVERT: A 495 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: A 816 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8444 (m) REVERT: B 84 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7084 (mm) REVERT: B 270 LEU cc_start: 0.9207 (mp) cc_final: 0.8964 (mp) REVERT: B 592 PHE cc_start: 0.7733 (t80) cc_final: 0.7373 (t80) REVERT: B 613 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: B 740 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7966 (ttm) REVERT: B 773 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6915 (tm-30) REVERT: B 850 ILE cc_start: 0.7970 (mm) cc_final: 0.7605 (mm) REVERT: B 869 MET cc_start: 0.8720 (ptt) cc_final: 0.8366 (ptt) REVERT: B 873 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7962 (t80) REVERT: B 955 ASN cc_start: 0.8612 (m110) cc_final: 0.8288 (t0) REVERT: B 966 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 1092 GLU cc_start: 0.8172 (pm20) cc_final: 0.7951 (pm20) REVERT: C 918 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: C 996 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9074 (mm) REVERT: C 1037 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8939 (t) outliers start: 110 outliers final: 70 residues processed: 263 average time/residue: 0.3322 time to fit residues: 146.6504 Evaluate side-chains 222 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 142 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 228 optimal weight: 0.0980 chunk 126 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B1010 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26407 Z= 0.289 Angle : 0.657 8.602 35940 Z= 0.332 Chirality : 0.049 0.591 4248 Planarity : 0.004 0.061 4557 Dihedral : 8.043 100.293 4767 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 4.58 % Allowed : 23.17 % Favored : 72.25 % 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: -1.47 (0.15), residues: 3159 helix: 1.22 (0.20), residues: 708 sheet: -1.16 (0.20), residues: 618 loop : -1.88 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.017 0.001 PHE B 92 TYR 0.028 0.002 TYR B 495 ARG 0.004 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 140 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7710 (m-80) cc_final: 0.7283 (m-80) REVERT: A 495 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: A 775 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8224 (t0) REVERT: A 816 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.6469 (m) REVERT: B 84 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7166 (mm) REVERT: B 270 LEU cc_start: 0.9226 (mp) cc_final: 0.8967 (mp) REVERT: B 592 PHE cc_start: 0.7723 (t80) cc_final: 0.7409 (t80) REVERT: B 613 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: B 697 MET cc_start: 0.7843 (tpp) cc_final: 0.7556 (tpp) REVERT: B 740 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7887 (ttm) REVERT: B 773 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6977 (tm-30) REVERT: B 869 MET cc_start: 0.8774 (ptt) cc_final: 0.8535 (ptt) REVERT: B 955 ASN cc_start: 0.8562 (m110) cc_final: 0.8296 (t0) REVERT: C 918 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: C 1037 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8978 (t) outliers start: 127 outliers final: 85 residues processed: 255 average time/residue: 0.3175 time to fit residues: 137.9932 Evaluate side-chains 226 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 133 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 8.9990 chunk 276 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 506 GLN B 628 GLN B 853 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26407 Z= 0.218 Angle : 0.628 10.284 35940 Z= 0.316 Chirality : 0.048 0.600 4248 Planarity : 0.005 0.112 4557 Dihedral : 7.722 99.460 4767 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 4.14 % Allowed : 23.86 % Favored : 72.00 % 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: -1.34 (0.15), residues: 3159 helix: 1.35 (0.20), residues: 696 sheet: -1.07 (0.20), residues: 602 loop : -1.79 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.017 0.001 PHE A 201 TYR 0.023 0.001 TYR B 495 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 156 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6417 (mmp) cc_final: 0.5420 (mmp) REVERT: A 456 PHE cc_start: 0.7666 (m-80) cc_final: 0.7289 (m-80) REVERT: A 495 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: B 84 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7217 (mm) REVERT: B 270 LEU cc_start: 0.9232 (mp) cc_final: 0.8980 (mp) REVERT: B 592 PHE cc_start: 0.7648 (t80) cc_final: 0.7362 (t80) REVERT: B 613 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: B 740 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7914 (ttm) REVERT: B 773 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6946 (tm-30) REVERT: B 873 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7910 (t80) REVERT: C 544 ASN cc_start: 0.8252 (t0) cc_final: 0.8051 (t0) REVERT: C 918 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: C 996 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9101 (mm) REVERT: C 1037 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8957 (t) outliers start: 115 outliers final: 77 residues processed: 258 average time/residue: 0.3179 time to fit residues: 140.5933 Evaluate side-chains 219 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 134 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 306 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 40.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN C 360 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26407 Z= 0.189 Angle : 0.620 9.145 35940 Z= 0.311 Chirality : 0.048 0.608 4248 Planarity : 0.004 0.054 4557 Dihedral : 7.503 97.922 4767 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 3.78 % Allowed : 24.29 % Favored : 71.93 % 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: -1.28 (0.15), residues: 3159 helix: 1.33 (0.20), residues: 711 sheet: -1.06 (0.20), residues: 607 loop : -1.73 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 104 HIS 0.003 0.001 HIS B 207 PHE 0.014 0.001 PHE B 833 TYR 0.023 0.001 TYR B 495 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 159 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6568 (mmp) cc_final: 0.5685 (mmp) REVERT: A 456 PHE cc_start: 0.7701 (m-80) cc_final: 0.7321 (m-80) REVERT: A 495 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: A 1130 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8745 (pt) REVERT: B 84 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7194 (mm) REVERT: B 270 LEU cc_start: 0.9189 (mp) cc_final: 0.8948 (mp) REVERT: B 613 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: B 740 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: B 773 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 873 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7853 (t80) REVERT: C 918 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: C 996 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9098 (mm) REVERT: C 1037 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8937 (t) outliers start: 105 outliers final: 79 residues processed: 255 average time/residue: 0.3201 time to fit residues: 138.4577 Evaluate side-chains 225 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 137 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 194 optimal weight: 0.9990 chunk 208 optimal weight: 0.3980 chunk 151 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 853 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26407 Z= 0.168 Angle : 0.622 9.326 35940 Z= 0.310 Chirality : 0.048 0.609 4248 Planarity : 0.004 0.052 4557 Dihedral : 7.319 96.135 4767 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 3.50 % Allowed : 24.68 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3159 helix: 1.38 (0.20), residues: 711 sheet: -0.94 (0.20), residues: 618 loop : -1.71 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 633 HIS 0.003 0.001 HIS B 207 PHE 0.014 0.001 PHE B 833 TYR 0.023 0.001 TYR B 495 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 166 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6468 (mmp) cc_final: 0.5622 (mmp) REVERT: A 406 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: A 456 PHE cc_start: 0.7672 (m-80) cc_final: 0.7292 (m-80) REVERT: A 495 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: A 591 SER cc_start: 0.8180 (t) cc_final: 0.7825 (p) REVERT: A 1130 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8752 (pt) REVERT: B 84 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7186 (mm) REVERT: B 242 LEU cc_start: 0.6603 (mm) cc_final: 0.6043 (tp) REVERT: B 270 LEU cc_start: 0.9165 (mp) cc_final: 0.8916 (mp) REVERT: B 613 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: B 740 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: B 773 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7449 (tm-30) REVERT: B 873 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7823 (t80) REVERT: C 556 ASN cc_start: 0.8887 (m110) cc_final: 0.8323 (t0) REVERT: C 918 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: C 996 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9076 (mm) REVERT: C 1037 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8900 (t) outliers start: 97 outliers final: 71 residues processed: 257 average time/residue: 0.3131 time to fit residues: 138.2927 Evaluate side-chains 225 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 144 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN B 965 GLN B1011 GLN B1106 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 26407 Z= 0.436 Angle : 0.750 9.447 35940 Z= 0.379 Chirality : 0.051 0.599 4248 Planarity : 0.005 0.047 4557 Dihedral : 7.797 100.384 4767 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.88 % Favored : 92.09 % Rotamer: Outliers : 3.82 % Allowed : 24.79 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3159 helix: 1.03 (0.19), residues: 713 sheet: -1.08 (0.20), residues: 612 loop : -1.86 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 633 HIS 0.006 0.001 HIS B 207 PHE 0.028 0.002 PHE A 592 TYR 0.027 0.002 TYR A 351 ARG 0.006 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 141 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7949 (m-40) cc_final: 0.7103 (t0) REVERT: A 177 MET cc_start: 0.6553 (mmp) cc_final: 0.5657 (mmp) REVERT: A 246 ARG cc_start: 0.1749 (OUTLIER) cc_final: -0.1938 (mpt180) REVERT: A 406 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: A 456 PHE cc_start: 0.7444 (m-80) cc_final: 0.7099 (m-80) REVERT: A 495 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: A 1039 ARG cc_start: 0.9549 (OUTLIER) cc_final: 0.9210 (mtm180) REVERT: A 1130 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8845 (pt) REVERT: B 270 LEU cc_start: 0.9279 (mp) cc_final: 0.9022 (mp) REVERT: B 697 MET cc_start: 0.8065 (mmm) cc_final: 0.7756 (mmm) REVERT: B 773 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 976 VAL cc_start: 0.9264 (t) cc_final: 0.9056 (p) REVERT: B 1012 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9331 (mt) REVERT: C 918 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: C 955 ASN cc_start: 0.8722 (m-40) cc_final: 0.8337 (t0) REVERT: C 985 ASP cc_start: 0.7784 (m-30) cc_final: 0.7306 (m-30) REVERT: C 1037 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9063 (t) outliers start: 106 outliers final: 83 residues processed: 239 average time/residue: 0.3167 time to fit residues: 129.3114 Evaluate side-chains 222 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 131 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.7980 chunk 302 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26407 Z= 0.209 Angle : 0.661 10.664 35940 Z= 0.331 Chirality : 0.049 0.614 4248 Planarity : 0.004 0.051 4557 Dihedral : 7.465 97.541 4767 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.57 % Rotamer: Outliers : 3.14 % Allowed : 25.37 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3159 helix: 1.22 (0.20), residues: 717 sheet: -1.05 (0.20), residues: 614 loop : -1.77 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.020 0.001 PHE A 592 TYR 0.026 0.001 TYR A 351 ARG 0.006 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 152 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7816 (m-40) cc_final: 0.6914 (t0) REVERT: A 177 MET cc_start: 0.6461 (mmp) cc_final: 0.5618 (mmp) REVERT: A 246 ARG cc_start: 0.1675 (OUTLIER) cc_final: -0.1951 (mpt180) REVERT: A 406 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: A 456 PHE cc_start: 0.7424 (m-80) cc_final: 0.7094 (m-80) REVERT: A 495 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: A 1130 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8762 (pt) REVERT: B 270 LEU cc_start: 0.9250 (mp) cc_final: 0.8991 (mp) REVERT: B 697 MET cc_start: 0.8097 (mmm) cc_final: 0.7783 (mmm) REVERT: B 773 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 873 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 417 ASN cc_start: 0.8163 (p0) cc_final: 0.7924 (t0) REVERT: C 918 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: C 955 ASN cc_start: 0.8725 (m-40) cc_final: 0.8432 (t0) REVERT: C 985 ASP cc_start: 0.7601 (m-30) cc_final: 0.7182 (m-30) REVERT: C 996 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9107 (mm) REVERT: C 1037 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8903 (t) outliers start: 87 outliers final: 72 residues processed: 233 average time/residue: 0.3174 time to fit residues: 127.2197 Evaluate side-chains 221 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 141 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.066316 restraints weight = 85284.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.068308 restraints weight = 49204.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069592 restraints weight = 34238.120| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26407 Z= 0.195 Angle : 0.642 10.002 35940 Z= 0.320 Chirality : 0.048 0.606 4248 Planarity : 0.004 0.052 4557 Dihedral : 7.287 97.042 4767 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 3.24 % Allowed : 25.37 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3159 helix: 1.34 (0.20), residues: 714 sheet: -1.08 (0.20), residues: 637 loop : -1.75 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 104 HIS 0.014 0.001 HIS A 66 PHE 0.032 0.001 PHE A 592 TYR 0.025 0.001 TYR A 351 ARG 0.005 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.06 seconds wall clock time: 80 minutes 45.21 seconds (4845.21 seconds total)