Starting phenix.real_space_refine on Fri Aug 9 16:39:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wq0_37732/08_2024/8wq0_37732.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wq0_37732/08_2024/8wq0_37732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wq0_37732/08_2024/8wq0_37732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wq0_37732/08_2024/8wq0_37732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wq0_37732/08_2024/8wq0_37732.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wq0_37732/08_2024/8wq0_37732.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 132 5.16 5 C 16968 2.51 5 N 4329 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 728": "OD1" <-> "OD2" Residue "A PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A ASP 962": "OD1" <-> "OD2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 644": "OD1" <-> "OD2" Residue "B PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 826": "OD1" <-> "OD2" Residue "B TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 973": "OE1" <-> "OE2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 962": "OD1" <-> "OD2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C GLU 973": "OE1" <-> "OE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26750 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8485 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 1 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8485 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 1 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8485 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 13.65, per 1000 atoms: 0.51 Number of scatterers: 26750 At special positions: 0 Unit cell: (147.165, 140.72, 174.02, 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 132 16.00 O 5321 8.00 N 4329 7.00 C 16968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.02 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.04 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 590 " " NAG A1303 " - " ASN A 358 " " NAG A1304 " - " ASN A 145 " " NAG A1305 " - " ASN A 692 " " NAG A1306 " - " ASN A1057 " " NAG A1307 " - " ASN A 159 " " NAG B1301 " - " ASN B 145 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 590 " " NAG B1304 " - " ASN B 358 " " NAG B1305 " - " ASN B 692 " " NAG B1306 " - " ASN B1057 " " NAG B1307 " - " ASN B 159 " " NAG B1308 " - " ASN B1081 " " NAG C1301 " - " ASN C 145 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 590 " " NAG C1304 " - " ASN C 358 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 159 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 120 " " NAG F 1 " - " ASN A 603 " " NAG G 1 " - " ASN A1081 " " NAG H 1 " - " ASN A1117 " " NAG I 1 " - " ASN A 784 " " NAG J 1 " - " ASN A 110 " " NAG K 1 " - " ASN A 228 " " NAG L 1 " - " ASN A 270 " " NAG M 1 " - " ASN A 700 " " NAG N 1 " - " ASN A 319 " " NAG O 1 " - " ASN B 66 " " NAG P 1 " - " ASN B 110 " " NAG Q 1 " - " ASN B 120 " " NAG R 1 " - " ASN B 319 " " NAG S 1 " - " ASN B 700 " " NAG T 1 " - " ASN B1117 " " NAG U 1 " - " ASN B 784 " " NAG V 1 " - " ASN B 228 " " NAG W 1 " - " ASN B 270 " " NAG X 1 " - " ASN B 603 " " NAG Y 1 " - " ASN C 66 " " NAG Z 1 " - " ASN C 110 " " NAG a 1 " - " ASN C 120 " " NAG b 1 " - " ASN C 228 " " NAG c 1 " - " ASN C 270 " " NAG d 1 " - " ASN C 319 " " NAG e 1 " - " ASN C 692 " " NAG f 1 " - " ASN C 700 " " NAG g 1 " - " ASN C1057 " " NAG h 1 " - " ASN C1081 " " NAG i 1 " - " ASN C1117 " " NAG j 1 " - " ASN C 784 " Time building additional restraints: 11.51 Conformation dependent library (CDL) restraints added in 4.5 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 49 sheets defined 24.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.550A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.354A pdb=" N ARG A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 743 through 766 Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.610A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.819A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 Processing helix chain 'A' and resid 928 through 949 removed outlier: 3.850A pdb=" N LEU A 945 " --> pdb=" O ALA A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 968 through 1016 removed outlier: 4.137A pdb=" N VAL A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.640A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.395A pdb=" N ARG B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 729 through 739 Processing helix chain 'B' and resid 742 through 766 removed outlier: 3.617A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.628A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 826 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.006A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 948 Processing helix chain 'B' and resid 949 through 951 No H-bonds generated for 'chain 'B' and resid 949 through 951' Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 968 through 1015 removed outlier: 3.868A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.570A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 393 through 398 removed outlier: 4.321A pdb=" N ARG C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 729 through 739 Processing helix chain 'C' and resid 742 through 766 removed outlier: 3.669A pdb=" N LEU C 746 " --> pdb=" O PHE C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.684A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 868 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 892 Processing helix chain 'C' and resid 895 through 902 removed outlier: 4.004A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 Processing helix chain 'C' and resid 949 through 951 No H-bonds generated for 'chain 'C' and resid 949 through 951' Processing helix chain 'C' and resid 959 through 965 Processing helix chain 'C' and resid 968 through 1015 removed outlier: 3.836A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.029A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.029A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 73 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A 76 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 60 removed outlier: 3.978A pdb=" N ASP A 275 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.293A pdb=" N PHE A 139 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL A 140 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.826A pdb=" N ASN A 231 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A 104 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 233 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP A 102 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 235 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 130 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS A 160 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU A 132 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N PHE A 158 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 4.384A pdb=" N LYS A 312 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 552 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.323A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 511 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.323A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN A 382 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 503 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB2, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.236A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 672 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 659 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.630A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.559A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA A1038 " --> pdb=" O GLY A1042 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A1044 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A1046 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1034 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1048 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.559A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A1059 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.450A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 770 through 772 Processing sheet with id=AB8, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB9, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 4.085A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.978A pdb=" N THR B 32 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 53 through 60 removed outlier: 4.083A pdb=" N ASP B 275 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.353A pdb=" N PHE B 139 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 140 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.513A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 237 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 99 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN B 130 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 160 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLU B 132 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N PHE B 158 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 299 through 302 Processing sheet with id=AC6, first strand: chain 'B' and resid 312 through 316 removed outlier: 4.366A pdb=" N LYS B 312 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP B 561 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.266A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 511 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.266A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN B 382 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU B 503 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AD1, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.174A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN B 672 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 657 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 684 through 686 removed outlier: 6.552A pdb=" N ALA B 684 " --> pdb=" O MET C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.737A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.737A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.353A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AD7, first strand: chain 'B' and resid 1103 through 1105 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.979A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 53 through 60 removed outlier: 3.975A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.371A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 removed outlier: 7.061A pdb=" N ASN C 231 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 104 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG C 233 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP C 102 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 235 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASN C 130 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS C 160 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU C 132 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N PHE C 158 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AE4, first strand: chain 'C' and resid 312 through 316 removed outlier: 4.357A pdb=" N LYS C 312 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.093A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.093A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN C 382 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU C 503 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AE8, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.255A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 672 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 657 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.732A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.732A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR C1059 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.383A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AF4, first strand: chain 'C' and resid 1103 through 1105 1088 hydrogen bonds defined for protein. 2997 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.99 Time building geometry restraints manager: 12.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8444 1.34 - 1.47: 7117 1.47 - 1.60: 11627 1.60 - 1.73: 0 1.73 - 1.85: 174 Bond restraints: 27362 Sorted by residual: bond pdb=" CA ASN A 159 " pdb=" C ASN A 159 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.34e-02 5.57e+03 3.39e+01 bond pdb=" C LEU B 413 " pdb=" N PRO B 414 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.22e-02 6.72e+03 9.45e+00 bond pdb=" C ARG C 450 " pdb=" N PRO C 451 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.20e-02 6.94e+03 6.78e+00 bond pdb=" C PHE A 317 " pdb=" N PRO A 318 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.25e-02 6.40e+03 6.19e+00 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 27357 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.03: 652 106.03 - 113.18: 15203 113.18 - 120.33: 9503 120.33 - 127.48: 11674 127.48 - 134.64: 210 Bond angle restraints: 37242 Sorted by residual: angle pdb=" C ASN A 159 " pdb=" N CYS A 160 " pdb=" CA CYS A 160 " ideal model delta sigma weight residual 122.73 111.11 11.62 1.62e+00 3.81e-01 5.15e+01 angle pdb=" C PHE A 317 " pdb=" N PRO A 318 " pdb=" CA PRO A 318 " ideal model delta sigma weight residual 120.21 114.26 5.95 9.60e-01 1.09e+00 3.84e+01 angle pdb=" C PHE C 317 " pdb=" N PRO C 318 " pdb=" CA PRO C 318 " ideal model delta sigma weight residual 120.03 114.11 5.92 9.90e-01 1.02e+00 3.58e+01 angle pdb=" N SER A 106 " pdb=" CA SER A 106 " pdb=" C SER A 106 " ideal model delta sigma weight residual 111.36 117.74 -6.38 1.09e+00 8.42e-01 3.43e+01 angle pdb=" C ASP A1122 " pdb=" N PRO A1123 " pdb=" CA PRO A1123 " ideal model delta sigma weight residual 119.56 114.45 5.11 1.01e+00 9.80e-01 2.56e+01 ... (remaining 37237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 16225 21.48 - 42.96: 1058 42.96 - 64.44: 190 64.44 - 85.92: 62 85.92 - 107.40: 28 Dihedral angle restraints: 17563 sinusoidal: 8053 harmonic: 9510 Sorted by residual: dihedral pdb=" CB CYS A 129 " pdb=" SG CYS A 129 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 20.66 72.34 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 743 " pdb=" CB CYS A 743 " ideal model delta sinusoidal sigma weight residual -86.00 -149.40 63.40 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 604 " pdb=" SG CYS B 604 " pdb=" SG CYS B 636 " pdb=" CB CYS B 636 " ideal model delta sinusoidal sigma weight residual 93.00 135.79 -42.79 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 17560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4403 0.195 - 0.389: 46 0.389 - 0.584: 6 0.584 - 0.778: 0 0.778 - 0.973: 2 Chirality restraints: 4457 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.98e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.20e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 ... (remaining 4454 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.334 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG A1306 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.308 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG B1308 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " -0.300 2.00e-02 2.50e+03 2.59e-01 8.39e+02 pdb=" C7 NAG B1305 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.207 2.00e-02 2.50e+03 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4029 2.76 - 3.30: 24133 3.30 - 3.83: 44407 3.83 - 4.37: 54764 4.37 - 4.90: 92581 Nonbonded interactions: 219914 Sorted by model distance: nonbonded pdb=" OH TYR B 42 " pdb=" O HIS B 59 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 42 " pdb=" O HIS A 59 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR C 42 " pdb=" O HIS C 59 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 371 " pdb=" OD1 ASP C 968 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP A 968 " pdb=" OG SER C 371 " model vdw 2.257 3.040 ... (remaining 219909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1127 or resid 1301 through 1306)) selection = (chain 'B' and (resid 19 through 1127 or resid 1301 through 1306)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'Q' selection = chain 'S' selection = chain 'a' selection = chain 'f' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 73.530 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.004 0.078 27362 Z= 0.275 Angle : 0.668 11.623 37242 Z= 0.351 Chirality : 0.059 0.973 4457 Planarity : 0.018 0.285 4731 Dihedral : 15.232 107.399 11308 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.26 % Allowed : 15.08 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3252 helix: 0.83 (0.19), residues: 675 sheet: 0.70 (0.18), residues: 765 loop : -0.58 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 869 HIS 0.002 0.001 HIS A1031 PHE 0.017 0.001 PHE A 104 TYR 0.031 0.001 TYR C1121 ARG 0.004 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 399 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8217 (mmm) cc_final: 0.7680 (mmm) REVERT: A 118 MET cc_start: 0.7802 (pp-130) cc_final: 0.7461 (ptt) REVERT: A 135 ASP cc_start: 0.7088 (m-30) cc_final: 0.6494 (m-30) REVERT: A 163 GLU cc_start: 0.7678 (tp30) cc_final: 0.7477 (mp0) REVERT: A 201 TYR cc_start: 0.8017 (t80) cc_final: 0.7549 (t80) REVERT: A 307 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7356 (mtm180) REVERT: A 383 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8391 (t) REVERT: A 467 PRO cc_start: 0.7603 (Cg_exo) cc_final: 0.7302 (Cg_endo) REVERT: A 693 ASN cc_start: 0.8548 (p0) cc_final: 0.8054 (p0) REVERT: A 777 LEU cc_start: 0.7800 (pp) cc_final: 0.7478 (mm) REVERT: A 831 ASP cc_start: 0.6972 (t0) cc_final: 0.6567 (t0) REVERT: A 832 LEU cc_start: 0.8167 (mt) cc_final: 0.7779 (mp) REVERT: A 878 GLN cc_start: 0.8334 (pt0) cc_final: 0.7767 (tm130) REVERT: A 916 GLN cc_start: 0.8168 (mt0) cc_final: 0.7945 (mt0) REVERT: A 997 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8302 (mtt90) REVERT: A 1026 CYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8663 (m) REVERT: A 1091 ASN cc_start: 0.8473 (m-40) cc_final: 0.8169 (m-40) REVERT: B 46 ASP cc_start: 0.8111 (m-30) cc_final: 0.7811 (m-30) REVERT: B 82 ILE cc_start: 0.8482 (mt) cc_final: 0.8234 (mt) REVERT: B 108 MET cc_start: 0.8179 (mmm) cc_final: 0.7840 (mmm) REVERT: B 135 ASP cc_start: 0.7032 (m-30) cc_final: 0.6268 (m-30) REVERT: B 181 LYS cc_start: 0.5851 (tptm) cc_final: 0.5586 (ttmt) REVERT: B 191 LYS cc_start: 0.8332 (tptm) cc_final: 0.8097 (ttpp) REVERT: B 201 TYR cc_start: 0.7808 (t80) cc_final: 0.7349 (t80) REVERT: B 307 ARG cc_start: 0.7360 (mtm180) cc_final: 0.6517 (mtp180) REVERT: B 312 LYS cc_start: 0.7150 (mttt) cc_final: 0.6890 (mttm) REVERT: B 382 ASN cc_start: 0.7903 (m-40) cc_final: 0.7605 (m-40) REVERT: B 467 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7329 (Cg_endo) REVERT: B 569 SER cc_start: 0.7349 (m) cc_final: 0.7133 (t) REVERT: B 601 ASP cc_start: 0.7713 (m-30) cc_final: 0.7463 (m-30) REVERT: B 730 THR cc_start: 0.8489 (m) cc_final: 0.8174 (p) REVERT: B 737 LEU cc_start: 0.8050 (tt) cc_final: 0.7833 (mp) REVERT: B 777 LEU cc_start: 0.7836 (pp) cc_final: 0.7302 (mm) REVERT: B 831 ASP cc_start: 0.7108 (t0) cc_final: 0.6764 (t0) REVERT: B 832 LEU cc_start: 0.8361 (mt) cc_final: 0.8002 (mt) REVERT: B 878 GLN cc_start: 0.8177 (pt0) cc_final: 0.7499 (tm130) REVERT: B 1084 SER cc_start: 0.8052 (p) cc_final: 0.7754 (t) REVERT: B 1091 ASN cc_start: 0.8224 (m-40) cc_final: 0.7972 (m-40) REVERT: B 1119 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 135 ASP cc_start: 0.7216 (m-30) cc_final: 0.6562 (m-30) REVERT: C 201 TYR cc_start: 0.7727 (t80) cc_final: 0.7376 (t80) REVERT: C 307 ARG cc_start: 0.7618 (mtm180) cc_final: 0.6654 (mtp-110) REVERT: C 467 PRO cc_start: 0.7419 (Cg_exo) cc_final: 0.7153 (Cg_endo) REVERT: C 501 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8950 (m) REVERT: C 633 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7478 (tm-30) REVERT: C 693 ASN cc_start: 0.8489 (p0) cc_final: 0.8251 (p0) REVERT: C 731 GLU cc_start: 0.7851 (mp0) cc_final: 0.7547 (mt-10) REVERT: C 747 ASN cc_start: 0.8719 (m-40) cc_final: 0.8487 (m-40) REVERT: C 777 LEU cc_start: 0.7856 (pp) cc_final: 0.7443 (mm) REVERT: C 824 LEU cc_start: 0.7522 (mp) cc_final: 0.7287 (mp) REVERT: C 831 ASP cc_start: 0.6889 (t0) cc_final: 0.6520 (t0) REVERT: C 878 GLN cc_start: 0.8190 (pt0) cc_final: 0.7939 (tm-30) REVERT: C 935 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8662 (p) REVERT: C 985 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 1091 ASN cc_start: 0.8373 (m-40) cc_final: 0.8172 (m-40) outliers start: 64 outliers final: 26 residues processed: 449 average time/residue: 1.3349 time to fit residues: 699.7734 Evaluate side-chains 281 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1026 CYS Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 627 ASN A 672 GLN A 884 GLN A 938 ASN B 97 ASN B 113 GLN B 155 ASN B 348 ASN B 506 ASN B 884 GLN B 896 GLN B 916 GLN B 938 ASN C 97 ASN C 113 GLN C 155 ASN C 600 GLN C 896 GLN C 937 GLN C 938 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27362 Z= 0.279 Angle : 0.661 10.741 37242 Z= 0.336 Chirality : 0.048 0.253 4457 Planarity : 0.005 0.057 4731 Dihedral : 8.576 64.410 5507 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.49 % Allowed : 14.02 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3252 helix: 1.24 (0.19), residues: 726 sheet: 0.67 (0.18), residues: 771 loop : -0.74 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 869 HIS 0.006 0.002 HIS C1047 PHE 0.018 0.002 PHE A 630 TYR 0.029 0.002 TYR B1050 ARG 0.006 0.001 ARG B1022 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 255 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8295 (mmm) cc_final: 0.7767 (mmm) REVERT: A 118 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7598 (ptt) REVERT: A 135 ASP cc_start: 0.7229 (m-30) cc_final: 0.6557 (m-30) REVERT: A 201 TYR cc_start: 0.8091 (t80) cc_final: 0.7519 (t80) REVERT: A 307 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7274 (mtm180) REVERT: A 383 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8608 (t) REVERT: A 440 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: A 467 PRO cc_start: 0.7669 (Cg_exo) cc_final: 0.7413 (Cg_endo) REVERT: A 648 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 777 LEU cc_start: 0.7838 (pp) cc_final: 0.7473 (mm) REVERT: A 831 ASP cc_start: 0.6883 (t0) cc_final: 0.6590 (t0) REVERT: A 832 LEU cc_start: 0.8107 (mt) cc_final: 0.7765 (mp) REVERT: A 878 GLN cc_start: 0.8351 (pt0) cc_final: 0.7645 (tm-30) REVERT: A 884 GLN cc_start: 0.8796 (tt0) cc_final: 0.8567 (tt0) REVERT: A 916 GLN cc_start: 0.8306 (mt0) cc_final: 0.8102 (mt0) REVERT: A 940 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: A 973 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: A 997 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8494 (mtt90) REVERT: A 1091 ASN cc_start: 0.8598 (m-40) cc_final: 0.8315 (m-40) REVERT: B 46 ASP cc_start: 0.8077 (m-30) cc_final: 0.7777 (m-30) REVERT: B 127 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7389 (ttt90) REVERT: B 135 ASP cc_start: 0.7030 (m-30) cc_final: 0.6242 (m-30) REVERT: B 181 LYS cc_start: 0.5916 (tptm) cc_final: 0.5638 (ttmt) REVERT: B 201 TYR cc_start: 0.8065 (t80) cc_final: 0.7609 (t80) REVERT: B 307 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6560 (mtp180) REVERT: B 345 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7901 (ttt-90) REVERT: B 467 PRO cc_start: 0.7730 (Cg_exo) cc_final: 0.7419 (Cg_endo) REVERT: B 601 ASP cc_start: 0.7765 (m-30) cc_final: 0.7314 (m-30) REVERT: B 730 THR cc_start: 0.8356 (m) cc_final: 0.8072 (p) REVERT: B 737 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7765 (tp) REVERT: B 777 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7484 (mm) REVERT: B 831 ASP cc_start: 0.7066 (t0) cc_final: 0.6637 (t0) REVERT: B 940 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: B 966 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: B 1091 ASN cc_start: 0.8509 (m-40) cc_final: 0.8186 (m-40) REVERT: C 58 ASP cc_start: 0.7405 (t0) cc_final: 0.7163 (t70) REVERT: C 122 THR cc_start: 0.7503 (p) cc_final: 0.7301 (t) REVERT: C 135 ASP cc_start: 0.7245 (m-30) cc_final: 0.6550 (m-30) REVERT: C 201 TYR cc_start: 0.7952 (t80) cc_final: 0.7583 (t80) REVERT: C 307 ARG cc_start: 0.7618 (mtm180) cc_final: 0.6689 (mtp-110) REVERT: C 467 PRO cc_start: 0.7484 (Cg_exo) cc_final: 0.7248 (Cg_endo) REVERT: C 731 GLU cc_start: 0.7917 (mp0) cc_final: 0.7673 (mt-10) REVERT: C 737 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7504 (tt) REVERT: C 777 LEU cc_start: 0.7907 (pp) cc_final: 0.7510 (mm) REVERT: C 807 ASN cc_start: 0.8016 (m-40) cc_final: 0.7775 (m-40) REVERT: C 831 ASP cc_start: 0.7014 (t0) cc_final: 0.6719 (t0) REVERT: C 878 GLN cc_start: 0.8262 (pt0) cc_final: 0.7820 (tm-30) REVERT: C 940 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: C 985 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 1091 ASN cc_start: 0.8663 (m-40) cc_final: 0.8403 (m-40) outliers start: 99 outliers final: 47 residues processed: 328 average time/residue: 1.1748 time to fit residues: 457.2731 Evaluate side-chains 294 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 233 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 450 ARG Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 506 ASN B 738 GLN B 890 ASN B 916 GLN B1102 ASN C 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27362 Z= 0.198 Angle : 0.565 9.849 37242 Z= 0.290 Chirality : 0.045 0.245 4457 Planarity : 0.004 0.053 4731 Dihedral : 6.656 59.901 5491 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 2.96 % Allowed : 14.48 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3252 helix: 1.66 (0.19), residues: 708 sheet: 0.71 (0.18), residues: 780 loop : -0.63 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 869 HIS 0.003 0.001 HIS B 196 PHE 0.014 0.001 PHE A 630 TYR 0.023 0.001 TYR B1050 ARG 0.003 0.000 ARG B1022 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 243 time to evaluate : 2.837 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: A 108 MET cc_start: 0.8297 (mmm) cc_final: 0.7797 (mmm) REVERT: A 135 ASP cc_start: 0.7224 (m-30) cc_final: 0.6578 (m-30) REVERT: A 201 TYR cc_start: 0.8055 (t80) cc_final: 0.7474 (t80) REVERT: A 450 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8413 (mtt-85) REVERT: A 777 LEU cc_start: 0.7820 (pp) cc_final: 0.7463 (mm) REVERT: A 831 ASP cc_start: 0.6939 (t0) cc_final: 0.6708 (t0) REVERT: A 832 LEU cc_start: 0.8073 (mt) cc_final: 0.7739 (mp) REVERT: A 878 GLN cc_start: 0.8326 (pt0) cc_final: 0.7622 (tm-30) REVERT: A 890 ASN cc_start: 0.8641 (t0) cc_final: 0.8276 (m-40) REVERT: A 916 GLN cc_start: 0.8303 (mt0) cc_final: 0.8081 (mt0) REVERT: A 973 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: A 1091 ASN cc_start: 0.8633 (m-40) cc_final: 0.8331 (m-40) REVERT: B 46 ASP cc_start: 0.8120 (m-30) cc_final: 0.7800 (m-30) REVERT: B 55 LEU cc_start: 0.8715 (tp) cc_final: 0.8452 (mt) REVERT: B 135 ASP cc_start: 0.6935 (m-30) cc_final: 0.6198 (m-30) REVERT: B 181 LYS cc_start: 0.5939 (tptm) cc_final: 0.5458 (ttpt) REVERT: B 201 TYR cc_start: 0.7961 (t80) cc_final: 0.7511 (t80) REVERT: B 307 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6563 (mtp180) REVERT: B 433 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7419 (tp-100) REVERT: B 467 PRO cc_start: 0.7660 (Cg_exo) cc_final: 0.7365 (Cg_endo) REVERT: B 723 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8733 (ttp) REVERT: B 730 THR cc_start: 0.8397 (m) cc_final: 0.8100 (p) REVERT: B 737 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7780 (tp) REVERT: B 777 LEU cc_start: 0.7990 (pp) cc_final: 0.7472 (mm) REVERT: B 831 ASP cc_start: 0.7037 (t0) cc_final: 0.6590 (t0) REVERT: B 940 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: B 968 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: B 1091 ASN cc_start: 0.8589 (m-40) cc_final: 0.8291 (m-40) REVERT: C 58 ASP cc_start: 0.7421 (t0) cc_final: 0.7209 (t0) REVERT: C 122 THR cc_start: 0.7489 (p) cc_final: 0.7279 (t) REVERT: C 135 ASP cc_start: 0.7255 (m-30) cc_final: 0.6574 (m-30) REVERT: C 156 ASN cc_start: 0.5586 (t0) cc_final: 0.5319 (t0) REVERT: C 201 TYR cc_start: 0.7933 (t80) cc_final: 0.7510 (t80) REVERT: C 307 ARG cc_start: 0.7623 (mtm180) cc_final: 0.6705 (mtp-110) REVERT: C 467 PRO cc_start: 0.7395 (Cg_exo) cc_final: 0.7184 (Cg_endo) REVERT: C 731 GLU cc_start: 0.7908 (mp0) cc_final: 0.7665 (mt-10) REVERT: C 737 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7539 (tt) REVERT: C 777 LEU cc_start: 0.7910 (pp) cc_final: 0.7505 (mm) REVERT: C 794 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5596 (ptmt) REVERT: C 807 ASN cc_start: 0.7991 (m-40) cc_final: 0.7742 (m-40) REVERT: C 831 ASP cc_start: 0.6902 (t0) cc_final: 0.6543 (t0) REVERT: C 878 GLN cc_start: 0.8242 (pt0) cc_final: 0.7733 (tm-30) REVERT: C 940 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: C 985 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8208 (tm-30) REVERT: C 1091 ASN cc_start: 0.8695 (m-40) cc_final: 0.8433 (m-40) outliers start: 84 outliers final: 50 residues processed: 308 average time/residue: 1.1870 time to fit residues: 435.6590 Evaluate side-chains 289 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 229 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 ASN B 506 ASN B 738 GLN B 916 GLN B1102 ASN C 97 ASN C 433 GLN C 938 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27362 Z= 0.273 Angle : 0.610 14.943 37242 Z= 0.318 Chirality : 0.046 0.259 4457 Planarity : 0.005 0.053 4731 Dihedral : 6.283 59.802 5487 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 4.05 % Allowed : 13.42 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3252 helix: 1.42 (0.19), residues: 732 sheet: 0.59 (0.17), residues: 786 loop : -0.75 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 869 HIS 0.004 0.001 HIS A 196 PHE 0.016 0.002 PHE C 630 TYR 0.025 0.002 TYR B1050 ARG 0.005 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 232 time to evaluate : 2.929 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: A 119 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8245 (t0) REVERT: A 201 TYR cc_start: 0.8031 (t80) cc_final: 0.7584 (t80) REVERT: A 648 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 777 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7558 (mm) REVERT: A 794 LYS cc_start: 0.6088 (ttmt) cc_final: 0.5661 (ptmt) REVERT: A 831 ASP cc_start: 0.6915 (t0) cc_final: 0.6633 (t0) REVERT: A 832 LEU cc_start: 0.8029 (mt) cc_final: 0.7697 (mp) REVERT: A 878 GLN cc_start: 0.8281 (pt0) cc_final: 0.7603 (tm-30) REVERT: A 916 GLN cc_start: 0.8332 (mt0) cc_final: 0.8115 (mt0) REVERT: A 940 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: A 973 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: A 1091 ASN cc_start: 0.8769 (m-40) cc_final: 0.8399 (m-40) REVERT: A 1119 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8286 (p) REVERT: B 46 ASP cc_start: 0.8108 (m-30) cc_final: 0.7797 (m-30) REVERT: B 135 ASP cc_start: 0.7030 (m-30) cc_final: 0.6261 (m-30) REVERT: B 181 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5611 (ttpt) REVERT: B 201 TYR cc_start: 0.7937 (t80) cc_final: 0.7567 (t80) REVERT: B 307 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6577 (mtp180) REVERT: B 433 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7489 (tp-100) REVERT: B 467 PRO cc_start: 0.7564 (Cg_exo) cc_final: 0.7287 (Cg_endo) REVERT: B 723 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (ttp) REVERT: B 730 THR cc_start: 0.8394 (m) cc_final: 0.8087 (p) REVERT: B 737 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7764 (tt) REVERT: B 777 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7572 (mm) REVERT: B 831 ASP cc_start: 0.7109 (t0) cc_final: 0.6674 (t0) REVERT: B 940 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: B 968 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: B 1091 ASN cc_start: 0.8698 (m-40) cc_final: 0.8364 (m-40) REVERT: C 58 ASP cc_start: 0.7395 (t0) cc_final: 0.7146 (t0) REVERT: C 201 TYR cc_start: 0.7929 (t80) cc_final: 0.7489 (t80) REVERT: C 307 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6591 (mtp-110) REVERT: C 569 SER cc_start: 0.7679 (m) cc_final: 0.7467 (t) REVERT: C 633 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7837 (mm-40) REVERT: C 702 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8772 (t) REVERT: C 731 GLU cc_start: 0.7934 (mp0) cc_final: 0.7682 (mt-10) REVERT: C 777 LEU cc_start: 0.8064 (pp) cc_final: 0.7794 (pt) REVERT: C 794 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5785 (ptmt) REVERT: C 807 ASN cc_start: 0.8045 (m-40) cc_final: 0.7792 (m-40) REVERT: C 831 ASP cc_start: 0.6872 (t0) cc_final: 0.6467 (t0) REVERT: C 878 GLN cc_start: 0.8219 (pt0) cc_final: 0.7794 (tm-30) REVERT: C 940 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: C 971 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: C 985 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 1033 MET cc_start: 0.9196 (ptm) cc_final: 0.8929 (ptm) outliers start: 115 outliers final: 57 residues processed: 318 average time/residue: 1.2282 time to fit residues: 461.8023 Evaluate side-chains 292 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 218 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 938 ASN B 425 ASN B 506 ASN B 916 GLN C 97 ASN C 938 ASN C1091 ASN C1102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 27362 Z= 0.390 Angle : 0.688 12.590 37242 Z= 0.360 Chirality : 0.050 0.273 4457 Planarity : 0.005 0.055 4731 Dihedral : 6.808 59.976 5487 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 4.44 % Allowed : 13.04 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3252 helix: 1.20 (0.19), residues: 732 sheet: 0.33 (0.17), residues: 816 loop : -0.86 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 424 HIS 0.007 0.002 HIS A 196 PHE 0.019 0.002 PHE C 77 TYR 0.025 0.002 TYR B1050 ARG 0.006 0.001 ARG B1022 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 220 time to evaluate : 2.879 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 119 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8356 (t0) REVERT: A 127 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6535 (ttp80) REVERT: A 201 TYR cc_start: 0.8006 (t80) cc_final: 0.7553 (t80) REVERT: A 440 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8555 (mttp) REVERT: A 648 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 777 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 831 ASP cc_start: 0.6939 (t0) cc_final: 0.6615 (t0) REVERT: A 832 LEU cc_start: 0.8014 (mt) cc_final: 0.7695 (mp) REVERT: A 890 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: A 916 GLN cc_start: 0.8357 (mt0) cc_final: 0.8136 (mt0) REVERT: A 940 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: A 973 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: A 1033 MET cc_start: 0.9337 (ptm) cc_final: 0.9057 (ptp) REVERT: B 127 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7490 (ttt90) REVERT: B 201 TYR cc_start: 0.7966 (t80) cc_final: 0.7637 (t80) REVERT: B 307 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6597 (mtp180) REVERT: B 382 ASN cc_start: 0.7794 (m-40) cc_final: 0.7485 (t0) REVERT: B 433 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7487 (tp-100) REVERT: B 467 PRO cc_start: 0.7571 (Cg_exo) cc_final: 0.7309 (Cg_endo) REVERT: B 723 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8698 (ttp) REVERT: B 730 THR cc_start: 0.8425 (m) cc_final: 0.8111 (p) REVERT: B 737 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7742 (tt) REVERT: B 777 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7619 (mm) REVERT: B 831 ASP cc_start: 0.7262 (t0) cc_final: 0.6946 (t0) REVERT: B 926 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7459 (t) REVERT: B 940 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: B 968 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: C 25 ASP cc_start: 0.5827 (OUTLIER) cc_final: 0.5528 (p0) REVERT: C 58 ASP cc_start: 0.7336 (t0) cc_final: 0.7084 (t70) REVERT: C 201 TYR cc_start: 0.8061 (t80) cc_final: 0.7605 (t80) REVERT: C 307 ARG cc_start: 0.7546 (mtm180) cc_final: 0.6751 (mtp180) REVERT: C 569 SER cc_start: 0.7975 (m) cc_final: 0.7702 (t) REVERT: C 663 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7379 (p) REVERT: C 702 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (t) REVERT: C 731 GLU cc_start: 0.7952 (mp0) cc_final: 0.7707 (mt-10) REVERT: C 737 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7642 (tt) REVERT: C 777 LEU cc_start: 0.8083 (pp) cc_final: 0.7824 (pt) REVERT: C 794 LYS cc_start: 0.6286 (ttpp) cc_final: 0.5889 (ptmt) REVERT: C 807 ASN cc_start: 0.8075 (m-40) cc_final: 0.7813 (m-40) REVERT: C 831 ASP cc_start: 0.6922 (t0) cc_final: 0.6486 (t0) REVERT: C 940 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: C 971 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: C 985 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8240 (tm-30) outliers start: 126 outliers final: 73 residues processed: 321 average time/residue: 1.1816 time to fit residues: 451.7967 Evaluate side-chains 305 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 210 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 260 optimal weight: 0.0470 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 506 ASN B 916 GLN B 988 GLN B1091 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27362 Z= 0.207 Angle : 0.578 14.943 37242 Z= 0.302 Chirality : 0.044 0.260 4457 Planarity : 0.004 0.052 4731 Dihedral : 6.308 58.643 5487 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 3.74 % Allowed : 14.24 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3252 helix: 1.44 (0.19), residues: 732 sheet: 0.43 (0.17), residues: 786 loop : -0.81 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 424 HIS 0.002 0.001 HIS C1031 PHE 0.016 0.001 PHE C 630 TYR 0.023 0.001 TYR B1050 ARG 0.002 0.000 ARG B1022 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 225 time to evaluate : 2.832 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: A 99 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7001 (mm) REVERT: A 201 TYR cc_start: 0.7999 (t80) cc_final: 0.7576 (t80) REVERT: A 476 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 648 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 777 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7555 (mm) REVERT: A 831 ASP cc_start: 0.6899 (t0) cc_final: 0.6632 (t0) REVERT: A 832 LEU cc_start: 0.8043 (mt) cc_final: 0.7724 (mp) REVERT: A 916 GLN cc_start: 0.8342 (mt0) cc_final: 0.8109 (mt0) REVERT: A 940 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: A 973 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: A 1033 MET cc_start: 0.9326 (ptm) cc_final: 0.9049 (ptp) REVERT: B 55 LEU cc_start: 0.8724 (tp) cc_final: 0.8431 (mt) REVERT: B 181 LYS cc_start: 0.6130 (ttmt) cc_final: 0.5786 (ttpt) REVERT: B 201 TYR cc_start: 0.7961 (t80) cc_final: 0.7657 (t80) REVERT: B 307 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6702 (mtp180) REVERT: B 467 PRO cc_start: 0.7600 (Cg_exo) cc_final: 0.7348 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: B 702 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8760 (p) REVERT: B 730 THR cc_start: 0.8406 (m) cc_final: 0.8092 (p) REVERT: B 737 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7831 (tp) REVERT: B 777 LEU cc_start: 0.8154 (pp) cc_final: 0.7656 (mm) REVERT: B 831 ASP cc_start: 0.7183 (t0) cc_final: 0.6742 (t0) REVERT: B 832 LEU cc_start: 0.8243 (mt) cc_final: 0.8004 (mt) REVERT: B 926 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7506 (t) REVERT: B 940 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: B 968 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: B 1084 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7595 (t) REVERT: C 58 ASP cc_start: 0.7388 (t0) cc_final: 0.7173 (t0) REVERT: C 118 MET cc_start: 0.8071 (ptt) cc_final: 0.7805 (ptm) REVERT: C 135 ASP cc_start: 0.6797 (m-30) cc_final: 0.6011 (m-30) REVERT: C 201 TYR cc_start: 0.8037 (t80) cc_final: 0.7610 (t80) REVERT: C 307 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6665 (mtp-110) REVERT: C 569 SER cc_start: 0.7794 (m) cc_final: 0.7560 (t) REVERT: C 633 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7909 (mm-40) REVERT: C 663 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7428 (p) REVERT: C 702 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8753 (t) REVERT: C 731 GLU cc_start: 0.7934 (mp0) cc_final: 0.7695 (mt-10) REVERT: C 777 LEU cc_start: 0.8057 (pp) cc_final: 0.7795 (pt) REVERT: C 794 LYS cc_start: 0.6241 (ttpp) cc_final: 0.5848 (ptmt) REVERT: C 807 ASN cc_start: 0.8043 (m-40) cc_final: 0.7795 (m-40) REVERT: C 831 ASP cc_start: 0.6814 (t0) cc_final: 0.6371 (t0) REVERT: C 940 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: C 971 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: C 985 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8214 (tm-30) outliers start: 106 outliers final: 60 residues processed: 303 average time/residue: 1.1484 time to fit residues: 415.1394 Evaluate side-chains 293 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 216 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1084 SER Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 144 optimal weight: 0.0040 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 938 ASN A1091 ASN B 113 GLN B 506 ASN B 916 GLN C 884 GLN C 938 ASN C1102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27362 Z= 0.256 Angle : 0.602 13.862 37242 Z= 0.314 Chirality : 0.046 0.271 4457 Planarity : 0.005 0.052 4731 Dihedral : 6.347 59.787 5487 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 3.81 % Allowed : 14.27 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3252 helix: 1.43 (0.19), residues: 732 sheet: 0.42 (0.17), residues: 780 loop : -0.82 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 424 HIS 0.004 0.001 HIS B1047 PHE 0.014 0.002 PHE A 630 TYR 0.024 0.001 TYR B1050 ARG 0.004 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 216 time to evaluate : 3.185 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: A 99 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6983 (mm) REVERT: A 201 TYR cc_start: 0.7997 (t80) cc_final: 0.7577 (t80) REVERT: A 313 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: A 440 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8518 (mttp) REVERT: A 648 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 777 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7540 (mm) REVERT: A 831 ASP cc_start: 0.6905 (t0) cc_final: 0.6694 (t0) REVERT: A 832 LEU cc_start: 0.8037 (mt) cc_final: 0.7747 (mp) REVERT: A 916 GLN cc_start: 0.8359 (mt0) cc_final: 0.8124 (mt0) REVERT: A 940 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: A 973 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 1033 MET cc_start: 0.9326 (ptm) cc_final: 0.9062 (ptp) REVERT: B 181 LYS cc_start: 0.6120 (ttmt) cc_final: 0.5816 (ttpt) REVERT: B 201 TYR cc_start: 0.7935 (t80) cc_final: 0.7633 (t80) REVERT: B 307 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6695 (mtp180) REVERT: B 467 PRO cc_start: 0.7526 (Cg_exo) cc_final: 0.7278 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 702 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8789 (p) REVERT: B 723 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8717 (ttp) REVERT: B 737 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 777 LEU cc_start: 0.8171 (pp) cc_final: 0.7662 (mm) REVERT: B 831 ASP cc_start: 0.7199 (t0) cc_final: 0.6761 (t0) REVERT: B 926 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7636 (t) REVERT: B 940 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: B 968 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6550 (m-30) REVERT: C 58 ASP cc_start: 0.7397 (t0) cc_final: 0.7174 (t70) REVERT: C 135 ASP cc_start: 0.6781 (m-30) cc_final: 0.6033 (m-30) REVERT: C 201 TYR cc_start: 0.8041 (t80) cc_final: 0.7626 (t80) REVERT: C 307 ARG cc_start: 0.7485 (mtm180) cc_final: 0.6642 (mtp-110) REVERT: C 569 SER cc_start: 0.7886 (m) cc_final: 0.7643 (t) REVERT: C 633 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7884 (mm-40) REVERT: C 663 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (p) REVERT: C 702 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8770 (t) REVERT: C 731 GLU cc_start: 0.7943 (mp0) cc_final: 0.7692 (mt-10) REVERT: C 737 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7591 (tt) REVERT: C 777 LEU cc_start: 0.8069 (pp) cc_final: 0.7820 (pt) REVERT: C 794 LYS cc_start: 0.6349 (ttpp) cc_final: 0.5937 (ptmt) REVERT: C 807 ASN cc_start: 0.8053 (m-40) cc_final: 0.7795 (m-40) REVERT: C 831 ASP cc_start: 0.6820 (t0) cc_final: 0.6384 (t0) REVERT: C 940 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: C 971 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: C 985 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 1033 MET cc_start: 0.9142 (ptm) cc_final: 0.8855 (ptm) outliers start: 108 outliers final: 71 residues processed: 302 average time/residue: 1.1529 time to fit residues: 416.3501 Evaluate side-chains 302 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 212 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1084 SER Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 938 ASN B 506 ASN B 916 GLN C 97 ASN C 425 ASN C 884 GLN C 938 ASN C1102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27362 Z= 0.216 Angle : 0.570 12.549 37242 Z= 0.299 Chirality : 0.044 0.268 4457 Planarity : 0.004 0.051 4731 Dihedral : 6.242 59.100 5487 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.95 % Allowed : 14.38 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3252 helix: 1.49 (0.19), residues: 732 sheet: 0.43 (0.17), residues: 780 loop : -0.80 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 424 HIS 0.003 0.001 HIS C1031 PHE 0.015 0.001 PHE A 630 TYR 0.023 0.001 TYR B1050 ARG 0.003 0.000 ARG B1022 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 212 time to evaluate : 3.014 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: A 99 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6948 (mm) REVERT: A 201 TYR cc_start: 0.7991 (t80) cc_final: 0.7579 (t80) REVERT: A 313 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: A 440 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: A 777 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7539 (mm) REVERT: A 831 ASP cc_start: 0.6902 (t0) cc_final: 0.6645 (t0) REVERT: A 832 LEU cc_start: 0.8033 (mt) cc_final: 0.7740 (mp) REVERT: A 916 GLN cc_start: 0.8351 (mt0) cc_final: 0.8114 (mt0) REVERT: A 940 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: A 973 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: A 1033 MET cc_start: 0.9325 (ptm) cc_final: 0.9055 (ptp) REVERT: A 1089 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: B 55 LEU cc_start: 0.8767 (tp) cc_final: 0.8433 (mt) REVERT: B 181 LYS cc_start: 0.6120 (ttmt) cc_final: 0.5832 (ttpt) REVERT: B 201 TYR cc_start: 0.7930 (t80) cc_final: 0.7636 (t80) REVERT: B 307 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6693 (mtp180) REVERT: B 467 PRO cc_start: 0.7463 (Cg_exo) cc_final: 0.7216 (Cg_endo) REVERT: B 594 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6877 (tp30) REVERT: B 702 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8738 (p) REVERT: B 723 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8706 (ttp) REVERT: B 737 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 777 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7632 (mm) REVERT: B 831 ASP cc_start: 0.7185 (t0) cc_final: 0.6726 (t0) REVERT: B 832 LEU cc_start: 0.8250 (mt) cc_final: 0.8007 (mt) REVERT: B 926 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7658 (t) REVERT: B 940 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: B 968 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6544 (m-30) REVERT: B 1084 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7593 (t) REVERT: C 58 ASP cc_start: 0.7348 (t0) cc_final: 0.7135 (t0) REVERT: C 135 ASP cc_start: 0.6773 (m-30) cc_final: 0.6030 (m-30) REVERT: C 201 TYR cc_start: 0.8032 (t80) cc_final: 0.7609 (t80) REVERT: C 307 ARG cc_start: 0.7540 (mtm180) cc_final: 0.6662 (mtp-110) REVERT: C 569 SER cc_start: 0.7797 (m) cc_final: 0.7559 (t) REVERT: C 633 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7875 (mm-40) REVERT: C 663 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7422 (p) REVERT: C 702 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8745 (t) REVERT: C 731 GLU cc_start: 0.7928 (mp0) cc_final: 0.7672 (mt-10) REVERT: C 737 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7586 (tt) REVERT: C 777 LEU cc_start: 0.8058 (pp) cc_final: 0.7811 (pt) REVERT: C 794 LYS cc_start: 0.6324 (ttpp) cc_final: 0.5903 (ptmt) REVERT: C 807 ASN cc_start: 0.8037 (m-40) cc_final: 0.7782 (m-40) REVERT: C 831 ASP cc_start: 0.6806 (t0) cc_final: 0.6373 (t0) REVERT: C 940 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: C 985 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 1033 MET cc_start: 0.9099 (ptm) cc_final: 0.8812 (ptm) outliers start: 112 outliers final: 73 residues processed: 301 average time/residue: 1.1536 time to fit residues: 414.2680 Evaluate side-chains 302 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 209 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1084 SER Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 938 ASN B 506 ASN B 916 GLN B1102 ASN C 97 ASN C 884 GLN C 938 ASN C1102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27362 Z= 0.293 Angle : 0.618 15.468 37242 Z= 0.324 Chirality : 0.046 0.280 4457 Planarity : 0.005 0.051 4731 Dihedral : 6.413 59.802 5487 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 3.84 % Allowed : 14.73 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3252 helix: 1.40 (0.19), residues: 732 sheet: 0.48 (0.17), residues: 762 loop : -0.81 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.004 0.001 HIS B1047 PHE 0.014 0.002 PHE A 630 TYR 0.024 0.002 TYR B1050 ARG 0.004 0.001 ARG B1022 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 208 time to evaluate : 2.975 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: A 99 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6913 (mm) REVERT: A 201 TYR cc_start: 0.7997 (t80) cc_final: 0.7574 (t80) REVERT: A 440 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8540 (mttp) REVERT: A 777 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7552 (mm) REVERT: A 831 ASP cc_start: 0.6912 (t0) cc_final: 0.6697 (t0) REVERT: A 832 LEU cc_start: 0.8043 (mt) cc_final: 0.7744 (mp) REVERT: A 916 GLN cc_start: 0.8384 (mt0) cc_final: 0.8162 (mt0) REVERT: A 940 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: A 973 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: A 1033 MET cc_start: 0.9329 (ptm) cc_final: 0.9063 (ptp) REVERT: B 181 LYS cc_start: 0.6052 (ttmt) cc_final: 0.5795 (ttpt) REVERT: B 201 TYR cc_start: 0.7941 (t80) cc_final: 0.7642 (t80) REVERT: B 307 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6697 (mtp180) REVERT: B 467 PRO cc_start: 0.7412 (Cg_exo) cc_final: 0.7187 (Cg_endo) REVERT: B 594 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6887 (tp30) REVERT: B 702 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 737 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7756 (tt) REVERT: B 777 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7636 (mm) REVERT: B 831 ASP cc_start: 0.7225 (t0) cc_final: 0.6930 (t0) REVERT: B 926 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7692 (t) REVERT: B 940 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: B 968 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6564 (m-30) REVERT: C 58 ASP cc_start: 0.7394 (t0) cc_final: 0.7173 (t70) REVERT: C 135 ASP cc_start: 0.6760 (m-30) cc_final: 0.6015 (m-30) REVERT: C 201 TYR cc_start: 0.8036 (t80) cc_final: 0.7616 (t80) REVERT: C 307 ARG cc_start: 0.7542 (mtm180) cc_final: 0.6659 (mtp-110) REVERT: C 569 SER cc_start: 0.7917 (m) cc_final: 0.7663 (t) REVERT: C 633 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7892 (mm-40) REVERT: C 663 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7306 (p) REVERT: C 702 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8769 (t) REVERT: C 731 GLU cc_start: 0.7900 (mp0) cc_final: 0.7645 (mt-10) REVERT: C 737 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7600 (tt) REVERT: C 777 LEU cc_start: 0.8075 (pp) cc_final: 0.7839 (pt) REVERT: C 794 LYS cc_start: 0.6330 (ttpp) cc_final: 0.6082 (ptpt) REVERT: C 807 ASN cc_start: 0.8058 (m-40) cc_final: 0.7800 (m-40) REVERT: C 831 ASP cc_start: 0.6823 (t0) cc_final: 0.6384 (t0) REVERT: C 940 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: C 985 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 1033 MET cc_start: 0.9145 (ptm) cc_final: 0.8860 (ptm) outliers start: 109 outliers final: 80 residues processed: 299 average time/residue: 1.2069 time to fit residues: 431.3365 Evaluate side-chains 303 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 207 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1084 SER Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1067 GLU Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 5.9990 chunk 307 optimal weight: 0.0870 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 257 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 0.0970 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 ASN B 506 ASN B 916 GLN C 97 ASN C 884 GLN C 938 ASN C1102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27362 Z= 0.181 Angle : 0.555 13.740 37242 Z= 0.291 Chirality : 0.044 0.268 4457 Planarity : 0.004 0.051 4731 Dihedral : 6.112 59.770 5487 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 15.64 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3252 helix: 1.66 (0.19), residues: 714 sheet: 0.55 (0.18), residues: 750 loop : -0.68 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 424 HIS 0.002 0.001 HIS C1066 PHE 0.015 0.001 PHE A 630 TYR 0.022 0.001 TYR B1050 ARG 0.002 0.000 ARG C 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 210 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6865 (mm) REVERT: A 201 TYR cc_start: 0.7983 (t80) cc_final: 0.7564 (t80) REVERT: A 777 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7534 (mm) REVERT: A 831 ASP cc_start: 0.6897 (t0) cc_final: 0.6655 (t0) REVERT: A 832 LEU cc_start: 0.8023 (mt) cc_final: 0.7734 (mp) REVERT: A 916 GLN cc_start: 0.8346 (mt0) cc_final: 0.8109 (mt0) REVERT: A 940 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: A 973 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 1033 MET cc_start: 0.9320 (ptm) cc_final: 0.9091 (ptp) REVERT: B 55 LEU cc_start: 0.8749 (tp) cc_final: 0.8407 (mt) REVERT: B 181 LYS cc_start: 0.6133 (ttmt) cc_final: 0.5798 (ttpt) REVERT: B 201 TYR cc_start: 0.7948 (t80) cc_final: 0.7658 (t80) REVERT: B 307 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6665 (mtp180) REVERT: B 467 PRO cc_start: 0.7394 (Cg_exo) cc_final: 0.7174 (Cg_endo) REVERT: B 594 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6880 (tp30) REVERT: B 702 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8718 (p) REVERT: B 723 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8712 (ttp) REVERT: B 737 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7882 (tp) REVERT: B 777 LEU cc_start: 0.8160 (pp) cc_final: 0.7649 (mm) REVERT: B 831 ASP cc_start: 0.7133 (t0) cc_final: 0.6650 (t0) REVERT: B 832 LEU cc_start: 0.8238 (mt) cc_final: 0.7988 (mt) REVERT: B 926 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7711 (t) REVERT: B 940 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: B 968 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: C 135 ASP cc_start: 0.6738 (m-30) cc_final: 0.6004 (m-30) REVERT: C 201 TYR cc_start: 0.8016 (t80) cc_final: 0.7596 (t80) REVERT: C 307 ARG cc_start: 0.7538 (mtm180) cc_final: 0.6669 (mtp-110) REVERT: C 569 SER cc_start: 0.7738 (m) cc_final: 0.7508 (t) REVERT: C 633 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7868 (mm-40) REVERT: C 663 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7431 (p) REVERT: C 731 GLU cc_start: 0.7922 (mp0) cc_final: 0.7666 (mt-10) REVERT: C 777 LEU cc_start: 0.8078 (pp) cc_final: 0.7826 (pt) REVERT: C 807 ASN cc_start: 0.8039 (m-40) cc_final: 0.7787 (m-40) REVERT: C 831 ASP cc_start: 0.6798 (t0) cc_final: 0.6354 (t0) REVERT: C 940 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: C 985 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8192 (tm-30) REVERT: C 1002 ARG cc_start: 0.8480 (tpt170) cc_final: 0.7644 (ttm110) outliers start: 83 outliers final: 62 residues processed: 278 average time/residue: 1.2297 time to fit residues: 409.2022 Evaluate side-chains 283 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 208 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 938 ASN B 506 ASN B 916 GLN C 97 ASN ** C 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.099841 restraints weight = 32314.140| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.06 r_work: 0.2828 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27362 Z= 0.232 Angle : 0.598 16.743 37242 Z= 0.310 Chirality : 0.045 0.276 4457 Planarity : 0.005 0.057 4731 Dihedral : 6.439 67.209 5487 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 3.17 % Allowed : 15.47 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3252 helix: 1.52 (0.19), residues: 732 sheet: 0.50 (0.18), residues: 756 loop : -0.76 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.003 0.001 HIS B1047 PHE 0.013 0.001 PHE A 630 TYR 0.023 0.001 TYR B1050 ARG 0.003 0.000 ARG B1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8258.89 seconds wall clock time: 146 minutes 35.80 seconds (8795.80 seconds total)