Starting phenix.real_space_refine on Sun Mar 24 05:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v89_31794/03_2024/7v89_31794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v89_31794/03_2024/7v89_31794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v89_31794/03_2024/7v89_31794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v89_31794/03_2024/7v89_31794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v89_31794/03_2024/7v89_31794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v89_31794/03_2024/7v89_31794.pdb" } resolution = 2.8 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= -0.001 sd= 0.060 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 195 5.16 5 C 25472 2.51 5 N 6535 2.21 5 O 7832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40034 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "C" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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 Time building chain proxies: 20.24, per 1000 atoms: 0.51 Number of scatterers: 40034 At special positions: 0 Unit cell: (176, 150.7, 245.3, 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 195 16.00 O 7832 8.00 N 6535 7.00 C 25472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.04 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG 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 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 341 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 601 " " NAG C2003 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 432 " " NAG H2001 " - " ASN H 53 " " NAG H2002 " - " ASN H 90 " " NAG I 1 " - " ASN A 232 " " NAG J 1 " - " ASN A 280 " " NAG K 1 " - " ASN A 329 " " NAG L 1 " - " ASN A 341 " " NAG M 1 " - " ASN A 614 " " NAG N 1 " - " ASN A 707 " " NAG O 1 " - " ASN A 715 " " NAG P 1 " - " ASN A 799 " " NAG Q 1 " - " ASN A1072 " " NAG R 1 " - " ASN A1096 " " NAG S 1 " - " ASN A1132 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 163 " " NAG V 1 " - " ASN B 232 " " NAG W 1 " - " ASN B 280 " " NAG X 1 " - " ASN B 329 " " NAG Y 1 " - " ASN B 614 " " NAG Z 1 " - " ASN B 707 " " NAG a 1 " - " ASN B 715 " " NAG b 1 " - " ASN B 799 " " NAG c 1 " - " ASN B1072 " " NAG d 1 " - " ASN B1096 " " NAG e 1 " - " ASN B1132 " " NAG f 1 " - " ASN C 122 " " NAG g 1 " - " ASN C 163 " " NAG h 1 " - " ASN C 232 " " NAG i 1 " - " ASN C 280 " " NAG j 1 " - " ASN C 329 " " NAG k 1 " - " ASN C 341 " " NAG l 1 " - " ASN C 614 " " NAG m 1 " - " ASN C 707 " " NAG n 1 " - " ASN C 715 " " NAG o 1 " - " ASN C 799 " " NAG p 1 " - " ASN C1072 " " NAG q 1 " - " ASN C1096 " " NAG r 1 " - " ASN C1132 " " NAG s 1 " - " ASN F 90 " " NAG t 1 " - " ASN F 103 " " NAG u 1 " - " ASN F 322 " " NAG v 1 " - " ASN F 546 " " NAG w 1 " - " ASN H 322 " Time building additional restraints: 16.80 Conformation dependent library (CDL) restraints added in 9.3 seconds 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9156 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 54 sheets defined 40.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.278A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.533A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.661A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.329A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.586A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.532A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.952A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.833A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.508A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.978A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.197A pdb=" N ASN B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.037A pdb=" N TYR B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 757 through 781 removed outlier: 3.659A pdb=" N LEU B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.580A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 910 through 939 removed outlier: 4.266A pdb=" N LEU B 914 " --> pdb=" O THR B 910 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS B 919 " --> pdb=" O TYR B 915 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 920 " --> pdb=" O GLU B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.551A pdb=" N GLN B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 981 removed outlier: 3.517A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 5.015A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.922A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.589A pdb=" N VAL C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.510A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.375A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.916A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.262A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.562A pdb=" N SER C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 removed outlier: 3.729A pdb=" N TYR C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.131A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 781 Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.553A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.554A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 916 removed outlier: 4.191A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.588A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.088A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.559A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.533A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.726A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 103 through 107 removed outlier: 4.057A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 194 removed outlier: 3.748A pdb=" N LEU F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.896A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.605A pdb=" N LEU F 266 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 263 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.570A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.599A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.888A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 413 removed outlier: 3.989A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.147A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.561A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.709A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.415A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.868A pdb=" N CYS F 542 " --> pdb=" O LEU F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.586A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 3.968A pdb=" N SER F 563 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 560 through 564' Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.975A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.612A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 79 removed outlier: 3.707A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 removed outlier: 3.600A pdb=" N ALA G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.536A pdb=" N SER G 106 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.565A pdb=" N LEU G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 194 removed outlier: 4.495A pdb=" N LEU G 179 " --> pdb=" O GLN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 205 removed outlier: 3.857A pdb=" N TYR G 202 " --> pdb=" O ASP G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 218 through 229 removed outlier: 3.652A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 252 Processing helix chain 'G' and resid 264 through 268 removed outlier: 4.163A pdb=" N GLY G 268 " --> pdb=" O HIS G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 293 through 301 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 385 Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 397 through 412 removed outlier: 4.051A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 447 removed outlier: 3.849A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.561A pdb=" N ARG G 482 " --> pdb=" O TRP G 478 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 507 removed outlier: 3.505A pdb=" N VAL G 506 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER G 507 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 507' Processing helix chain 'G' and resid 512 through 532 removed outlier: 3.944A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 519 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU G 520 " --> pdb=" O TYR G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.877A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.723A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN G 599 " --> pdb=" O LEU G 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.988A pdb=" N GLU H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 79 removed outlier: 3.821A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.974A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 158 through 172 Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.376A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 218 through 229 removed outlier: 3.513A pdb=" N LEU H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 233 through 252 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 293 through 300 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 Processing helix chain 'H' and resid 365 through 386 Processing helix chain 'H' and resid 387 through 388 No H-bonds generated for 'chain 'H' and resid 387 through 388' Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.698A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 413 removed outlier: 4.258A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.767A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 removed outlier: 3.707A pdb=" N TRP H 477 " --> pdb=" O TRP H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.516A pdb=" N SER H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN H 508 " --> pdb=" O PHE H 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 503 through 508' Processing helix chain 'H' and resid 512 through 532 removed outlier: 4.112A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.657A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 removed outlier: 3.785A pdb=" N SER H 563 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 560 through 564' Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.535A pdb=" N LEU H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 597 removed outlier: 4.200A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.970A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.638A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 540 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.033A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.096A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLU A 132 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLN A 134 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ASN A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.596A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.787A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.766A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.289A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.703A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.595A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.464A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1092 through 1095 removed outlier: 4.792A pdb=" N GLN A1104 " --> pdb=" O GLU A1109 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU A1109 " --> pdb=" O GLN A1104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.963A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.084A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.125A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.572A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 323 through 324 removed outlier: 3.536A pdb=" N ASN B 540 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.747A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC9, first strand: chain 'B' and resid 571 through 574 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.309A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.888A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 726 removed outlier: 3.590A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.440A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD7, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 4.723A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.091A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.251A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.574A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE4, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.770A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE6, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE7, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.221A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.550A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.530A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF3, first strand: chain 'C' and resid 1092 through 1094 removed outlier: 4.769A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF5, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.258A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 132 through 133 Processing sheet with id=AF7, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AF8, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.174A pdb=" N ASN H 134 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU H 140 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 347 through 350 1737 hydrogen bonds defined for protein. 4869 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: 17.74 Time building geometry restraints manager: 18.06 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: 12708 1.34 - 1.46: 10214 1.46 - 1.58: 17783 1.58 - 1.70: 1 1.70 - 1.82: 282 Bond restraints: 40988 Sorted by residual: bond pdb=" CB PRO G 253 " pdb=" CG PRO G 253 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" C1 NAG p 1 " pdb=" O5 NAG p 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 40983 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.43: 806 105.43 - 112.59: 21426 112.59 - 119.75: 13168 119.75 - 126.92: 19822 126.92 - 134.08: 519 Bond angle restraints: 55741 Sorted by residual: angle pdb=" CA PRO G 253 " pdb=" N PRO G 253 " pdb=" CD PRO G 253 " ideal model delta sigma weight residual 112.00 101.36 10.64 1.40e+00 5.10e-01 5.78e+01 angle pdb=" N MET F 123 " pdb=" CA MET F 123 " pdb=" CB MET F 123 " ideal model delta sigma weight residual 110.30 117.23 -6.93 1.54e+00 4.22e-01 2.02e+01 angle pdb=" CA MET F 123 " pdb=" CB MET F 123 " pdb=" CG MET F 123 " ideal model delta sigma weight residual 114.10 122.55 -8.45 2.00e+00 2.50e-01 1.78e+01 angle pdb=" CB MET F 123 " pdb=" CG MET F 123 " pdb=" SD MET F 123 " ideal model delta sigma weight residual 112.70 124.19 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C THR F 122 " pdb=" N MET F 123 " pdb=" CA MET F 123 " ideal model delta sigma weight residual 120.68 114.21 6.47 1.70e+00 3.46e-01 1.45e+01 ... (remaining 55736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 23621 21.15 - 42.30: 1688 42.30 - 63.45: 259 63.45 - 84.60: 71 84.60 - 105.75: 20 Dihedral angle restraints: 25659 sinusoidal: 11442 harmonic: 14217 Sorted by residual: dihedral pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " pdb=" SG CYS B 758 " pdb=" CB CYS B 758 " ideal model delta sinusoidal sigma weight residual -86.00 3.30 -89.30 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 1.64 -87.64 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C 289 " pdb=" SG CYS C 289 " pdb=" SG CYS C 299 " pdb=" CB CYS C 299 " ideal model delta sinusoidal sigma weight residual -86.00 -172.93 86.93 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 25656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 6431 0.186 - 0.373: 5 0.373 - 0.559: 0 0.559 - 0.746: 0 0.746 - 0.932: 1 Chirality restraints: 6437 Sorted by residual: chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN C1096 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG v 1 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG v 1 " pdb=" O5 NAG v 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA PRO G 253 " pdb=" N PRO G 253 " pdb=" C PRO G 253 " pdb=" CB PRO G 253 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 6434 not shown) Planarity restraints: 7144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 252 " 0.062 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO G 253 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO G 253 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 253 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 25 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 26 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 134 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO H 135 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 135 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 135 " -0.029 5.00e-02 4.00e+02 ... (remaining 7141 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 900 2.68 - 3.24: 39186 3.24 - 3.79: 63024 3.79 - 4.35: 81668 4.35 - 4.90: 135186 Nonbonded interactions: 319964 Sorted by model distance: nonbonded pdb=" OG SER B 347 " pdb=" O ARG B 450 " model vdw 2.128 2.440 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.159 2.440 nonbonded pdb=" NH2 ARG F 482 " pdb=" O THR F 608 " model vdw 2.162 2.520 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.165 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.175 2.440 ... (remaining 319959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1144 or resid 2001 through 2003)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'F' and resid 19 through 614) selection = chain 'G' selection = (chain 'H' and resid 19 through 614) } 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: 4.470 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: 0.030 Extract box with map and model: 14.250 Check model and map are aligned: 0.630 Set scattering table: 0.370 Process input model: 109.740 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.920 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.003 0.162 40988 Z= 0.221 Angle : 0.578 11.487 55741 Z= 0.286 Chirality : 0.045 0.932 6437 Planarity : 0.004 0.087 7087 Dihedral : 14.389 105.748 16359 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.26 (0.12), residues: 4815 helix: 1.83 (0.13), residues: 1669 sheet: 0.43 (0.18), residues: 749 loop : -1.16 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 69 HIS 0.012 0.001 HIS F 401 PHE 0.030 0.001 PHE F 369 TYR 0.014 0.001 TYR A1065 ARG 0.009 0.000 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6240 (ttt90) REVERT: A 451 TYR cc_start: 0.7032 (p90) cc_final: 0.5931 (p90) REVERT: A 641 PHE cc_start: 0.7867 (t80) cc_final: 0.7611 (t80) REVERT: B 572 ASP cc_start: 0.7418 (m-30) cc_final: 0.7049 (m-30) REVERT: C 133 PHE cc_start: 0.7539 (m-80) cc_final: 0.7298 (m-80) REVERT: C 367 TYR cc_start: 0.8685 (t80) cc_final: 0.8285 (t80) REVERT: C 368 ASN cc_start: 0.8024 (m-40) cc_final: 0.7781 (p0) REVERT: C 513 PHE cc_start: 0.7334 (m-80) cc_final: 0.6926 (m-80) REVERT: F 123 MET cc_start: 0.8019 (pmm) cc_final: 0.7595 (ppp) REVERT: F 480 MET cc_start: 0.7727 (mpp) cc_final: 0.7403 (mpp) REVERT: F 527 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7644 (tp30) REVERT: G 26 LYS cc_start: 0.6277 (mttt) cc_final: 0.5954 (tppt) REVERT: G 152 MET cc_start: 0.0169 (ptt) cc_final: -0.0239 (mtp) REVERT: G 171 GLU cc_start: 0.1594 (pp20) cc_final: 0.1243 (mp0) REVERT: G 227 GLU cc_start: 0.4993 (pm20) cc_final: 0.4178 (pp20) REVERT: G 455 MET cc_start: 0.2934 (ppp) cc_final: 0.2689 (pp-130) REVERT: G 557 MET cc_start: 0.0646 (ttt) cc_final: 0.0349 (ptm) REVERT: G 573 VAL cc_start: 0.2416 (t) cc_final: 0.1750 (p) REVERT: G 581 VAL cc_start: 0.2408 (p) cc_final: 0.2061 (p) REVERT: G 586 ASN cc_start: 0.3753 (m-40) cc_final: 0.3084 (m-40) REVERT: H 111 ASP cc_start: 0.8482 (m-30) cc_final: 0.8251 (t70) REVERT: H 152 MET cc_start: 0.0266 (tmm) cc_final: -0.0106 (ttm) REVERT: H 297 MET cc_start: 0.2286 (pmm) cc_final: 0.1812 (pmm) REVERT: H 366 MET cc_start: 0.4107 (tpt) cc_final: 0.3718 (OUTLIER) REVERT: H 462 MET cc_start: 0.7631 (ptp) cc_final: 0.7251 (mmt) REVERT: H 474 MET cc_start: 0.1865 (ppp) cc_final: 0.0929 (ppp) REVERT: H 557 MET cc_start: 0.7439 (ppp) cc_final: 0.6787 (ppp) REVERT: H 572 ASN cc_start: 0.6787 (m-40) cc_final: 0.6192 (p0) REVERT: H 579 MET cc_start: 0.2622 (tpp) cc_final: 0.2261 (tpp) outliers start: 0 outliers final: 1 residues processed: 369 average time/residue: 1.3792 time to fit residues: 628.5687 Evaluate side-chains 206 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 6.9990 chunk 366 optimal weight: 40.0000 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 246 optimal weight: 40.0000 chunk 195 optimal weight: 0.8980 chunk 378 optimal weight: 0.0170 chunk 146 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 438 optimal weight: 30.0000 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN B 802 GLN B 912 ASN C 332 ASN C 412 GLN C 540 ASN C 955 GLN C1003 GLN C1104 GLN F 34 HIS ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40988 Z= 0.199 Angle : 0.573 10.292 55741 Z= 0.284 Chirality : 0.044 0.244 6437 Planarity : 0.004 0.056 7087 Dihedral : 7.655 87.935 7323 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 0.98 % Allowed : 7.98 % Favored : 91.03 % 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: 0.33 (0.12), residues: 4815 helix: 1.81 (0.13), residues: 1729 sheet: 0.53 (0.18), residues: 742 loop : -1.15 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 477 HIS 0.007 0.001 HIS F 34 PHE 0.025 0.001 PHE A 904 TYR 0.026 0.001 TYR H 385 ARG 0.009 0.000 ARG C1037 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 4.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7610 (mtm180) cc_final: 0.6268 (ttt90) REVERT: A 641 PHE cc_start: 0.7919 (t80) cc_final: 0.7661 (t80) REVERT: B 572 ASP cc_start: 0.7517 (m-30) cc_final: 0.7074 (m-30) REVERT: C 133 PHE cc_start: 0.7601 (m-80) cc_final: 0.7374 (m-80) REVERT: C 171 GLN cc_start: 0.8702 (mp10) cc_final: 0.7895 (tm130) REVERT: C 367 TYR cc_start: 0.8738 (t80) cc_final: 0.8342 (t80) REVERT: C 368 ASN cc_start: 0.8045 (m-40) cc_final: 0.7724 (p0) REVERT: C 450 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6383 (ttm-80) REVERT: F 123 MET cc_start: 0.8100 (pmm) cc_final: 0.7843 (ppp) REVERT: F 480 MET cc_start: 0.7228 (mpp) cc_final: 0.6935 (mpp) REVERT: G 26 LYS cc_start: 0.6313 (mttt) cc_final: 0.5977 (tppt) REVERT: G 152 MET cc_start: 0.0064 (ptt) cc_final: -0.0306 (mtp) REVERT: G 171 GLU cc_start: 0.1919 (pp20) cc_final: 0.1607 (mp0) REVERT: G 227 GLU cc_start: 0.4367 (pm20) cc_final: 0.3938 (pp20) REVERT: G 360 MET cc_start: 0.1437 (tpp) cc_final: 0.0246 (ptp) REVERT: G 462 MET cc_start: 0.1598 (ptt) cc_final: 0.1398 (ptp) REVERT: G 557 MET cc_start: 0.0678 (ttt) cc_final: 0.0361 (ptm) REVERT: G 573 VAL cc_start: 0.2441 (t) cc_final: 0.1762 (p) REVERT: H 111 ASP cc_start: 0.8485 (m-30) cc_final: 0.8248 (t70) REVERT: H 152 MET cc_start: 0.0350 (tmm) cc_final: -0.0118 (ttm) REVERT: H 297 MET cc_start: 0.2416 (pmm) cc_final: 0.2052 (pmm) REVERT: H 323 MET cc_start: 0.4403 (tmm) cc_final: 0.3840 (ppp) REVERT: H 366 MET cc_start: 0.4380 (tpt) cc_final: 0.3879 (tpp) REVERT: H 408 MET cc_start: 0.5166 (ppp) cc_final: 0.4959 (tmm) REVERT: H 462 MET cc_start: 0.7694 (ptp) cc_final: 0.7188 (mmt) REVERT: H 474 MET cc_start: 0.1846 (ppp) cc_final: 0.0649 (ppp) REVERT: H 557 MET cc_start: 0.7363 (ppp) cc_final: 0.6662 (ppp) REVERT: H 572 ASN cc_start: 0.6849 (m-40) cc_final: 0.6266 (p0) REVERT: H 579 MET cc_start: 0.2708 (tpp) cc_final: 0.2432 (tpp) outliers start: 42 outliers final: 19 residues processed: 249 average time/residue: 1.3873 time to fit residues: 429.7920 Evaluate side-chains 202 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 365 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 439 optimal weight: 40.0000 chunk 474 optimal weight: 20.0000 chunk 391 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 499 ASN A 899 GLN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN C 115 GLN C 446 ASN C 912 ASN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.106 40988 Z= 0.714 Angle : 0.797 12.891 55741 Z= 0.403 Chirality : 0.055 0.370 6437 Planarity : 0.006 0.063 7087 Dihedral : 7.943 85.508 7323 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 2.08 % Allowed : 12.22 % Favored : 85.70 % 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: -0.25 (0.12), residues: 4815 helix: 1.33 (0.12), residues: 1722 sheet: 0.19 (0.18), residues: 743 loop : -1.48 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 884 HIS 0.013 0.002 HIS A1056 PHE 0.044 0.003 PHE B 904 TYR 0.034 0.002 TYR C1065 ARG 0.017 0.001 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 192 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 876 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8821 (tt) REVERT: B 572 ASP cc_start: 0.7484 (m-30) cc_final: 0.6850 (m-30) REVERT: B 583 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7453 (mp) REVERT: B 894 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8779 (tp) REVERT: C 64 TRP cc_start: 0.7099 (t60) cc_final: 0.6636 (t60) REVERT: C 102 ARG cc_start: 0.5742 (mmp-170) cc_final: 0.5351 (ttm170) REVERT: C 133 PHE cc_start: 0.7620 (m-80) cc_final: 0.7378 (m-80) REVERT: C 198 TYR cc_start: 0.8742 (m-80) cc_final: 0.8425 (m-80) REVERT: C 367 TYR cc_start: 0.8676 (t80) cc_final: 0.8076 (t80) REVERT: C 368 ASN cc_start: 0.8063 (m-40) cc_final: 0.7667 (p0) REVERT: C 419 TYR cc_start: 0.7074 (m-10) cc_final: 0.6388 (m-10) REVERT: C 446 ASN cc_start: 0.7731 (t0) cc_final: 0.6957 (t0) REVERT: C 450 ARG cc_start: 0.7230 (mtm180) cc_final: 0.6521 (ttm-80) REVERT: C 738 MET cc_start: 0.8887 (ttt) cc_final: 0.8456 (ttt) REVERT: C 1038 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8737 (m) REVERT: F 123 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7829 (ppp) REVERT: F 579 MET cc_start: 0.0688 (OUTLIER) cc_final: -0.1196 (mtm) REVERT: G 26 LYS cc_start: 0.6209 (mttt) cc_final: 0.5766 (tppt) REVERT: G 152 MET cc_start: -0.0130 (ptt) cc_final: -0.0405 (mtp) REVERT: G 171 GLU cc_start: 0.2157 (pp20) cc_final: 0.1727 (mp0) REVERT: G 207 TYR cc_start: -0.0263 (OUTLIER) cc_final: -0.0645 (m-80) REVERT: G 227 GLU cc_start: 0.4460 (pm20) cc_final: 0.4060 (pp20) REVERT: G 360 MET cc_start: 0.1408 (tpp) cc_final: 0.0243 (ptm) REVERT: G 557 MET cc_start: 0.0500 (ttt) cc_final: 0.0222 (ptm) REVERT: G 573 VAL cc_start: 0.1924 (t) cc_final: 0.1186 (p) REVERT: H 152 MET cc_start: 0.0571 (tmm) cc_final: 0.0166 (ttm) REVERT: H 323 MET cc_start: 0.4524 (tmm) cc_final: 0.3718 (ppp) REVERT: H 366 MET cc_start: 0.4153 (tpt) cc_final: 0.3671 (OUTLIER) REVERT: H 462 MET cc_start: 0.7609 (ptp) cc_final: 0.7121 (mmt) REVERT: H 474 MET cc_start: 0.1780 (ppp) cc_final: 0.0885 (ppp) REVERT: H 557 MET cc_start: 0.7434 (ppp) cc_final: 0.6949 (ppp) REVERT: H 572 ASN cc_start: 0.6887 (m-40) cc_final: 0.6429 (p0) outliers start: 89 outliers final: 50 residues processed: 258 average time/residue: 1.2882 time to fit residues: 419.6163 Evaluate side-chains 229 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 173 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 784 LYS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1131 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain G residue 207 TYR Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 440 optimal weight: 9.9990 chunk 466 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 417 optimal weight: 50.0000 chunk 125 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN A 749 ASN A 912 ASN C 115 GLN C 540 ASN C1003 GLN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 ASN ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40988 Z= 0.181 Angle : 0.569 15.681 55741 Z= 0.282 Chirality : 0.044 0.274 6437 Planarity : 0.004 0.055 7087 Dihedral : 7.009 76.587 7323 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 1.76 % Allowed : 13.93 % Favored : 84.32 % 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 (0.12), residues: 4815 helix: 1.70 (0.13), residues: 1720 sheet: 0.33 (0.18), residues: 745 loop : -1.32 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 610 HIS 0.020 0.001 HIS G 239 PHE 0.016 0.001 PHE C1119 TYR 0.024 0.001 TYR H 385 ARG 0.004 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 187 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 ASP cc_start: 0.7637 (m-30) cc_final: 0.7306 (m-30) REVERT: B 114 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7806 (p) REVERT: B 572 ASP cc_start: 0.7362 (m-30) cc_final: 0.6775 (m-30) REVERT: C 133 PHE cc_start: 0.7625 (m-80) cc_final: 0.7380 (m-80) REVERT: C 171 GLN cc_start: 0.8727 (mp10) cc_final: 0.7688 (tm130) REVERT: C 198 TYR cc_start: 0.8582 (m-80) cc_final: 0.8184 (m-80) REVERT: C 367 TYR cc_start: 0.8690 (t80) cc_final: 0.8105 (t80) REVERT: C 368 ASN cc_start: 0.8171 (m-40) cc_final: 0.7809 (p0) REVERT: C 375 PHE cc_start: 0.8179 (t80) cc_final: 0.7861 (t80) REVERT: C 419 TYR cc_start: 0.7239 (m-10) cc_final: 0.6550 (m-10) REVERT: C 450 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6395 (ttm-80) REVERT: C 513 PHE cc_start: 0.7530 (m-80) cc_final: 0.7244 (m-80) REVERT: F 123 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7868 (ppp) REVERT: F 249 MET cc_start: 0.3678 (mmt) cc_final: 0.3371 (mpp) REVERT: F 366 MET cc_start: 0.4233 (mmp) cc_final: 0.3965 (mpp) REVERT: F 527 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8029 (tp30) REVERT: G 26 LYS cc_start: 0.6302 (mttt) cc_final: 0.5857 (tppt) REVERT: G 171 GLU cc_start: 0.1834 (pp20) cc_final: 0.1543 (mp0) REVERT: G 207 TYR cc_start: -0.0331 (OUTLIER) cc_final: -0.0577 (m-80) REVERT: G 227 GLU cc_start: 0.4504 (pm20) cc_final: 0.4100 (pp20) REVERT: G 360 MET cc_start: 0.1300 (tpp) cc_final: 0.0108 (ptm) REVERT: G 573 VAL cc_start: 0.1912 (t) cc_final: 0.1105 (p) REVERT: H 152 MET cc_start: 0.0561 (tmm) cc_final: 0.0153 (ttm) REVERT: H 323 MET cc_start: 0.4591 (tmm) cc_final: 0.3748 (ppp) REVERT: H 360 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.3894 (tmt) REVERT: H 366 MET cc_start: 0.4067 (tpt) cc_final: 0.3625 (OUTLIER) REVERT: H 462 MET cc_start: 0.7552 (ptp) cc_final: 0.7155 (mmt) REVERT: H 474 MET cc_start: 0.1499 (ppp) cc_final: 0.0660 (ppp) REVERT: H 557 MET cc_start: 0.7479 (ppp) cc_final: 0.6989 (ppp) REVERT: H 572 ASN cc_start: 0.6927 (m-40) cc_final: 0.6460 (p0) REVERT: H 579 MET cc_start: 0.2609 (mmt) cc_final: 0.1431 (tpp) outliers start: 75 outliers final: 37 residues processed: 246 average time/residue: 1.2985 time to fit residues: 403.4447 Evaluate side-chains 209 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 207 TYR Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 360 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 347 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 398 optimal weight: 40.0000 chunk 322 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 238 optimal weight: 10.0000 chunk 419 optimal weight: 0.0060 chunk 117 optimal weight: 0.8980 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 540 ASN C1003 GLN F 117 ASN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 40988 Z= 0.289 Angle : 0.604 16.837 55741 Z= 0.299 Chirality : 0.045 0.256 6437 Planarity : 0.004 0.060 7087 Dihedral : 6.793 73.689 7323 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.86 % Favored : 94.12 % Rotamer: Outliers : 2.39 % Allowed : 14.63 % Favored : 82.98 % 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 (0.12), residues: 4815 helix: 1.71 (0.12), residues: 1728 sheet: 0.35 (0.18), residues: 736 loop : -1.38 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 477 HIS 0.005 0.001 HIS B1062 PHE 0.020 0.002 PHE C 166 TYR 0.022 0.001 TYR C1065 ARG 0.010 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 177 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7558 (mtm180) cc_final: 0.6236 (ttt90) REVERT: A 572 ASP cc_start: 0.7704 (m-30) cc_final: 0.7340 (m-30) REVERT: A 876 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8803 (tt) REVERT: B 114 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7833 (p) REVERT: B 572 ASP cc_start: 0.7425 (m-30) cc_final: 0.6817 (m-30) REVERT: C 102 ARG cc_start: 0.5654 (mmp-170) cc_final: 0.5281 (ttm170) REVERT: C 133 PHE cc_start: 0.7637 (m-80) cc_final: 0.7371 (m-80) REVERT: C 171 GLN cc_start: 0.8709 (mp10) cc_final: 0.7654 (tm130) REVERT: C 198 TYR cc_start: 0.8610 (m-80) cc_final: 0.8219 (m-80) REVERT: C 367 TYR cc_start: 0.8686 (t80) cc_final: 0.8120 (t80) REVERT: C 368 ASN cc_start: 0.8172 (m-40) cc_final: 0.7793 (p0) REVERT: C 375 PHE cc_start: 0.8095 (t80) cc_final: 0.7844 (t80) REVERT: C 419 TYR cc_start: 0.7247 (m-10) cc_final: 0.6562 (m-10) REVERT: C 450 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6814 (ptm160) REVERT: C 513 PHE cc_start: 0.7513 (m-80) cc_final: 0.7249 (m-80) REVERT: C 558 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8855 (mp) REVERT: F 123 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7853 (ppp) REVERT: F 249 MET cc_start: 0.3806 (mmt) cc_final: 0.3523 (mpp) REVERT: G 26 LYS cc_start: 0.6311 (mttt) cc_final: 0.5862 (tppt) REVERT: G 171 GLU cc_start: 0.1843 (pp20) cc_final: 0.1507 (mp0) REVERT: G 207 TYR cc_start: -0.0641 (OUTLIER) cc_final: -0.0875 (m-80) REVERT: G 227 GLU cc_start: 0.4499 (pm20) cc_final: 0.4097 (pp20) REVERT: H 152 MET cc_start: 0.0523 (tmm) cc_final: 0.0200 (ttm) REVERT: H 297 MET cc_start: 0.2400 (OUTLIER) cc_final: 0.2155 (pmm) REVERT: H 323 MET cc_start: 0.4351 (tmm) cc_final: 0.3471 (ppp) REVERT: H 366 MET cc_start: 0.4205 (tpt) cc_final: 0.3757 (OUTLIER) REVERT: H 462 MET cc_start: 0.7557 (ptp) cc_final: 0.7149 (mmt) REVERT: H 474 MET cc_start: 0.1530 (ppp) cc_final: 0.0674 (ppp) REVERT: H 557 MET cc_start: 0.7438 (ppp) cc_final: 0.6748 (ppp) REVERT: H 572 ASN cc_start: 0.6932 (m-40) cc_final: 0.6485 (p0) REVERT: H 579 MET cc_start: 0.2641 (mmt) cc_final: 0.1552 (tpp) outliers start: 102 outliers final: 59 residues processed: 259 average time/residue: 1.2317 time to fit residues: 404.8529 Evaluate side-chains 237 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 173 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 207 TYR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 315 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 0.7980 chunk 420 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 274 optimal weight: 0.0970 chunk 115 optimal weight: 0.6980 chunk 467 optimal weight: 6.9990 chunk 387 optimal weight: 50.0000 chunk 216 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 overall best weight: 1.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1003 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 442 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 40988 Z= 0.250 Angle : 0.588 17.217 55741 Z= 0.289 Chirality : 0.044 0.262 6437 Planarity : 0.004 0.056 7087 Dihedral : 6.539 69.047 7323 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.42 % Favored : 94.56 % Rotamer: Outliers : 2.39 % Allowed : 15.96 % Favored : 81.65 % 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 (0.12), residues: 4815 helix: 1.79 (0.13), residues: 1710 sheet: 0.43 (0.19), residues: 718 loop : -1.35 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 477 HIS 0.011 0.001 HIS G 239 PHE 0.019 0.001 PHE C1119 TYR 0.022 0.001 TYR C1065 ARG 0.006 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 181 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7579 (mtm180) cc_final: 0.6263 (ttt90) REVERT: A 572 ASP cc_start: 0.7633 (m-30) cc_final: 0.7258 (m-30) REVERT: A 876 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8799 (tt) REVERT: B 114 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 572 ASP cc_start: 0.7415 (m-30) cc_final: 0.6793 (m-30) REVERT: B 894 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (tp) REVERT: C 133 PHE cc_start: 0.7675 (m-80) cc_final: 0.7443 (m-80) REVERT: C 171 GLN cc_start: 0.8686 (mp10) cc_final: 0.7613 (tm130) REVERT: C 198 TYR cc_start: 0.8626 (m-80) cc_final: 0.8258 (m-80) REVERT: C 367 TYR cc_start: 0.8689 (t80) cc_final: 0.8138 (t80) REVERT: C 368 ASN cc_start: 0.8157 (m-40) cc_final: 0.7766 (p0) REVERT: C 375 PHE cc_start: 0.8066 (t80) cc_final: 0.7844 (t80) REVERT: C 419 TYR cc_start: 0.7304 (m-10) cc_final: 0.6637 (m-10) REVERT: C 450 ARG cc_start: 0.7172 (mtm180) cc_final: 0.6843 (ptm160) REVERT: C 513 PHE cc_start: 0.7549 (m-80) cc_final: 0.7247 (m-80) REVERT: C 558 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 1011 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8584 (mm) REVERT: F 123 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7870 (ppp) REVERT: F 249 MET cc_start: 0.3787 (mmt) cc_final: 0.3526 (mpp) REVERT: F 366 MET cc_start: 0.4032 (mmp) cc_final: 0.3775 (mpp) REVERT: F 527 GLU cc_start: 0.8683 (tm-30) cc_final: 0.7979 (tp30) REVERT: G 26 LYS cc_start: 0.6313 (mttt) cc_final: 0.5860 (tppt) REVERT: G 171 GLU cc_start: 0.1838 (pp20) cc_final: 0.1508 (mp0) REVERT: G 227 GLU cc_start: 0.4494 (pm20) cc_final: 0.4125 (pp20) REVERT: G 360 MET cc_start: 0.1406 (tpp) cc_final: 0.0015 (ptp) REVERT: H 111 ASP cc_start: 0.8482 (m-30) cc_final: 0.8237 (t70) REVERT: H 152 MET cc_start: 0.0537 (tmm) cc_final: 0.0108 (ttm) REVERT: H 297 MET cc_start: 0.2404 (OUTLIER) cc_final: 0.2158 (pmm) REVERT: H 323 MET cc_start: 0.4323 (tmm) cc_final: 0.3520 (ppp) REVERT: H 366 MET cc_start: 0.4286 (tpt) cc_final: 0.3781 (OUTLIER) REVERT: H 462 MET cc_start: 0.7556 (ptp) cc_final: 0.7146 (mmt) REVERT: H 474 MET cc_start: 0.1511 (ppp) cc_final: 0.0660 (ppp) REVERT: H 557 MET cc_start: 0.7441 (ppp) cc_final: 0.6734 (ppp) REVERT: H 572 ASN cc_start: 0.7009 (m-40) cc_final: 0.6577 (p0) REVERT: H 579 MET cc_start: 0.2700 (mmt) cc_final: 0.1639 (tpp) outliers start: 102 outliers final: 65 residues processed: 264 average time/residue: 1.2419 time to fit residues: 417.6936 Evaluate side-chains 242 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 171 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 297 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 393 optimal weight: 0.0060 chunk 260 optimal weight: 0.8980 chunk 465 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 121 ASN C1003 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 40988 Z= 0.235 Angle : 0.580 17.262 55741 Z= 0.285 Chirality : 0.044 0.262 6437 Planarity : 0.004 0.056 7087 Dihedral : 6.354 64.782 7323 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 2.36 % Allowed : 16.57 % Favored : 81.06 % 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: 0.17 (0.12), residues: 4815 helix: 1.84 (0.13), residues: 1707 sheet: 0.46 (0.19), residues: 720 loop : -1.35 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 477 HIS 0.006 0.001 HIS G 239 PHE 0.020 0.001 PHE A 757 TYR 0.021 0.001 TYR C1065 ARG 0.005 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 179 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: A 450 ARG cc_start: 0.7637 (mtm180) cc_final: 0.6252 (ttt90) REVERT: A 572 ASP cc_start: 0.7627 (m-30) cc_final: 0.7291 (m-30) REVERT: A 876 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8814 (tt) REVERT: B 114 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7817 (p) REVERT: B 572 ASP cc_start: 0.7417 (m-30) cc_final: 0.6791 (m-30) REVERT: B 584 ASP cc_start: 0.7988 (t0) cc_final: 0.7375 (t0) REVERT: B 894 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8629 (tp) REVERT: C 133 PHE cc_start: 0.7684 (m-80) cc_final: 0.7444 (m-80) REVERT: C 198 TYR cc_start: 0.8610 (m-80) cc_final: 0.8241 (m-80) REVERT: C 367 TYR cc_start: 0.8694 (t80) cc_final: 0.8138 (t80) REVERT: C 368 ASN cc_start: 0.8162 (m-40) cc_final: 0.7753 (p0) REVERT: C 375 PHE cc_start: 0.8039 (t80) cc_final: 0.7821 (t80) REVERT: C 419 TYR cc_start: 0.7383 (m-10) cc_final: 0.6781 (m-10) REVERT: C 450 ARG cc_start: 0.7170 (mtm180) cc_final: 0.6852 (ptm160) REVERT: C 558 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8851 (mp) REVERT: F 123 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7876 (ppp) REVERT: F 366 MET cc_start: 0.4186 (mmp) cc_final: 0.3976 (mpp) REVERT: F 527 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8010 (tp30) REVERT: G 26 LYS cc_start: 0.6313 (mttt) cc_final: 0.5859 (tppt) REVERT: G 171 GLU cc_start: 0.1724 (pp20) cc_final: 0.1389 (mp0) REVERT: G 227 GLU cc_start: 0.4485 (pm20) cc_final: 0.4122 (pp20) REVERT: G 360 MET cc_start: 0.1344 (tpp) cc_final: 0.0059 (ptp) REVERT: H 111 ASP cc_start: 0.8480 (m-30) cc_final: 0.8236 (t70) REVERT: H 152 MET cc_start: 0.0590 (tmm) cc_final: 0.0151 (ttm) REVERT: H 297 MET cc_start: 0.2396 (OUTLIER) cc_final: 0.2150 (pmm) REVERT: H 323 MET cc_start: 0.4326 (tmm) cc_final: 0.3478 (ppp) REVERT: H 360 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.3916 (tmt) REVERT: H 366 MET cc_start: 0.4359 (tpt) cc_final: 0.3869 (OUTLIER) REVERT: H 462 MET cc_start: 0.7562 (ptp) cc_final: 0.7153 (mmt) REVERT: H 474 MET cc_start: 0.1495 (ppp) cc_final: 0.0653 (ppp) REVERT: H 557 MET cc_start: 0.7463 (ppp) cc_final: 0.6765 (ppp) REVERT: H 572 ASN cc_start: 0.7036 (m-40) cc_final: 0.6603 (p0) REVERT: H 579 MET cc_start: 0.2791 (mmt) cc_final: 0.1774 (tpp) outliers start: 101 outliers final: 70 residues processed: 262 average time/residue: 1.2224 time to fit residues: 410.9579 Evaluate side-chains 250 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 173 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 360 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 278 optimal weight: 0.6980 chunk 140 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 295 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 365 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN C1003 GLN G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 40988 Z= 0.189 Angle : 0.568 17.234 55741 Z= 0.278 Chirality : 0.043 0.265 6437 Planarity : 0.004 0.056 7087 Dihedral : 6.158 61.348 7323 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 2.32 % Allowed : 16.74 % Favored : 80.95 % 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: 0.25 (0.12), residues: 4815 helix: 1.91 (0.13), residues: 1706 sheet: 0.56 (0.19), residues: 719 loop : -1.33 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 477 HIS 0.005 0.001 HIS F 401 PHE 0.020 0.001 PHE G 308 TYR 0.019 0.001 TYR H 385 ARG 0.004 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 183 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: A 450 ARG cc_start: 0.7551 (mtm180) cc_final: 0.6238 (ttt90) REVERT: A 572 ASP cc_start: 0.7626 (m-30) cc_final: 0.7252 (m-30) REVERT: A 771 GLU cc_start: 0.7918 (tt0) cc_final: 0.7519 (tt0) REVERT: A 1111 GLN cc_start: 0.8356 (mt0) cc_final: 0.8064 (mt0) REVERT: B 114 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7803 (p) REVERT: B 572 ASP cc_start: 0.7416 (m-30) cc_final: 0.6793 (m-30) REVERT: B 584 ASP cc_start: 0.7967 (t0) cc_final: 0.7329 (t0) REVERT: B 894 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8594 (tp) REVERT: C 133 PHE cc_start: 0.7689 (m-80) cc_final: 0.7443 (m-80) REVERT: C 171 GLN cc_start: 0.8700 (mp10) cc_final: 0.7677 (tm130) REVERT: C 198 TYR cc_start: 0.8605 (m-80) cc_final: 0.8281 (m-80) REVERT: C 367 TYR cc_start: 0.8695 (t80) cc_final: 0.8156 (t80) REVERT: C 368 ASN cc_start: 0.8162 (m-40) cc_final: 0.7751 (p0) REVERT: C 419 TYR cc_start: 0.7394 (m-10) cc_final: 0.6793 (m-10) REVERT: C 450 ARG cc_start: 0.7195 (mtm180) cc_final: 0.6870 (ptm160) REVERT: G 26 LYS cc_start: 0.6381 (mttt) cc_final: 0.5916 (tppt) REVERT: G 227 GLU cc_start: 0.4463 (pm20) cc_final: 0.4108 (pp20) REVERT: G 360 MET cc_start: 0.1464 (tpp) cc_final: 0.0228 (ptp) REVERT: H 111 ASP cc_start: 0.8479 (m-30) cc_final: 0.8237 (t70) REVERT: H 123 MET cc_start: 0.3854 (ppp) cc_final: 0.3584 (pmm) REVERT: H 152 MET cc_start: 0.0589 (tmm) cc_final: 0.0111 (ttm) REVERT: H 297 MET cc_start: 0.2386 (OUTLIER) cc_final: 0.2140 (pmm) REVERT: H 323 MET cc_start: 0.4298 (tmm) cc_final: 0.3414 (ppp) REVERT: H 366 MET cc_start: 0.4358 (tpt) cc_final: 0.3869 (OUTLIER) REVERT: H 462 MET cc_start: 0.7572 (ptp) cc_final: 0.7154 (mmt) REVERT: H 474 MET cc_start: 0.1479 (ppp) cc_final: 0.0646 (ppp) REVERT: H 557 MET cc_start: 0.7479 (ppp) cc_final: 0.6755 (ppp) REVERT: H 572 ASN cc_start: 0.7037 (m-40) cc_final: 0.6606 (p0) REVERT: H 579 MET cc_start: 0.2710 (mmt) cc_final: 0.1667 (tpp) outliers start: 99 outliers final: 75 residues processed: 265 average time/residue: 1.2551 time to fit residues: 424.5968 Evaluate side-chains 251 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 173 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 315 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 30.0000 chunk 445 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 433 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 392 optimal weight: 4.9990 chunk 410 optimal weight: 5.9990 chunk 432 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 499 ASN B 121 ASN C 912 ASN C1003 GLN F 102 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 GLN ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 40988 Z= 0.500 Angle : 0.692 18.080 55741 Z= 0.344 Chirality : 0.049 0.278 6437 Planarity : 0.005 0.054 7087 Dihedral : 6.539 59.856 7323 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.46 % Favored : 93.52 % Rotamer: Outliers : 2.39 % Allowed : 17.13 % Favored : 80.48 % 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 (0.12), residues: 4815 helix: 1.67 (0.12), residues: 1711 sheet: 0.26 (0.19), residues: 724 loop : -1.45 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 477 HIS 0.012 0.002 HIS G 239 PHE 0.027 0.002 PHE A 757 TYR 0.028 0.002 TYR C1065 ARG 0.016 0.001 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 176 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: B 114 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7912 (p) REVERT: B 572 ASP cc_start: 0.7418 (m-30) cc_final: 0.6591 (m-30) REVERT: B 584 ASP cc_start: 0.8049 (t0) cc_final: 0.7567 (t0) REVERT: B 894 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (tp) REVERT: C 102 ARG cc_start: 0.6074 (mmp-170) cc_final: 0.5388 (ttm170) REVERT: C 133 PHE cc_start: 0.7644 (m-80) cc_final: 0.7372 (m-80) REVERT: C 198 TYR cc_start: 0.8649 (m-80) cc_final: 0.8291 (m-80) REVERT: C 367 TYR cc_start: 0.8688 (t80) cc_final: 0.8174 (t80) REVERT: C 368 ASN cc_start: 0.8102 (m-40) cc_final: 0.7730 (p0) REVERT: C 419 TYR cc_start: 0.7391 (m-10) cc_final: 0.6805 (m-10) REVERT: C 450 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6837 (ptm160) REVERT: C 513 PHE cc_start: 0.7291 (m-80) cc_final: 0.7074 (m-80) REVERT: C 738 MET cc_start: 0.8879 (ttt) cc_final: 0.8442 (ttt) REVERT: F 323 MET cc_start: 0.6815 (tmm) cc_final: 0.6453 (tpp) REVERT: F 527 GLU cc_start: 0.8691 (tm-30) cc_final: 0.7956 (tp30) REVERT: G 26 LYS cc_start: 0.6262 (mttt) cc_final: 0.5768 (tppt) REVERT: G 227 GLU cc_start: 0.4471 (pm20) cc_final: 0.4083 (pp20) REVERT: G 360 MET cc_start: 0.1500 (tpp) cc_final: 0.0276 (ptm) REVERT: H 111 ASP cc_start: 0.8463 (m-30) cc_final: 0.8238 (t70) REVERT: H 123 MET cc_start: 0.3929 (ppp) cc_final: 0.3298 (pmm) REVERT: H 152 MET cc_start: 0.0592 (tmm) cc_final: 0.0200 (ttm) REVERT: H 297 MET cc_start: 0.2294 (pmm) cc_final: 0.2029 (pmm) REVERT: H 315 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: H 323 MET cc_start: 0.4272 (tmm) cc_final: 0.3534 (ppp) REVERT: H 366 MET cc_start: 0.4402 (tpt) cc_final: 0.3921 (OUTLIER) REVERT: H 462 MET cc_start: 0.7559 (ptp) cc_final: 0.7127 (mmt) REVERT: H 474 MET cc_start: 0.1438 (ppp) cc_final: 0.0616 (ppp) REVERT: H 557 MET cc_start: 0.7458 (ppp) cc_final: 0.7156 (ttt) REVERT: H 572 ASN cc_start: 0.7043 (m-40) cc_final: 0.6648 (p0) outliers start: 102 outliers final: 77 residues processed: 266 average time/residue: 1.2817 time to fit residues: 437.3896 Evaluate side-chains 250 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 170 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 471 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 315 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 1.9990 chunk 458 optimal weight: 40.0000 chunk 279 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 7.9990 chunk 442 optimal weight: 0.7980 chunk 383 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 295 optimal weight: 0.5980 chunk 234 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN C1003 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 40988 Z= 0.185 Angle : 0.594 17.335 55741 Z= 0.291 Chirality : 0.044 0.298 6437 Planarity : 0.004 0.055 7087 Dihedral : 6.100 55.616 7323 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 1.76 % Allowed : 17.81 % Favored : 80.43 % 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: 0.18 (0.12), residues: 4815 helix: 1.85 (0.13), residues: 1709 sheet: 0.47 (0.19), residues: 733 loop : -1.37 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 163 HIS 0.005 0.001 HIS F 401 PHE 0.018 0.001 PHE A 757 TYR 0.019 0.001 TYR H 385 ARG 0.003 0.000 ARG C 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 182 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASP cc_start: 0.7611 (m-30) cc_final: 0.7234 (m-30) REVERT: A 771 GLU cc_start: 0.7919 (tt0) cc_final: 0.7542 (tt0) REVERT: A 1111 GLN cc_start: 0.8360 (mt0) cc_final: 0.8079 (mt0) REVERT: B 572 ASP cc_start: 0.7406 (m-30) cc_final: 0.6805 (m-30) REVERT: B 584 ASP cc_start: 0.7947 (t0) cc_final: 0.7308 (t0) REVERT: C 133 PHE cc_start: 0.7644 (m-80) cc_final: 0.7368 (m-80) REVERT: C 198 TYR cc_start: 0.8610 (m-80) cc_final: 0.8312 (m-80) REVERT: C 367 TYR cc_start: 0.8698 (t80) cc_final: 0.8206 (t80) REVERT: C 368 ASN cc_start: 0.8103 (m-40) cc_final: 0.7721 (p0) REVERT: C 419 TYR cc_start: 0.7391 (m-10) cc_final: 0.6806 (m-10) REVERT: F 323 MET cc_start: 0.6692 (tmm) cc_final: 0.6350 (tpp) REVERT: F 527 GLU cc_start: 0.8678 (tm-30) cc_final: 0.7962 (tp30) REVERT: G 26 LYS cc_start: 0.6291 (mttt) cc_final: 0.5809 (tppt) REVERT: G 227 GLU cc_start: 0.4463 (pm20) cc_final: 0.4109 (pp20) REVERT: G 360 MET cc_start: 0.1566 (tpp) cc_final: 0.0185 (ptp) REVERT: G 480 MET cc_start: 0.2228 (pp-130) cc_final: 0.1621 (mtp) REVERT: H 111 ASP cc_start: 0.8480 (m-30) cc_final: 0.8233 (t70) REVERT: H 123 MET cc_start: 0.3898 (ppp) cc_final: 0.3289 (pmm) REVERT: H 152 MET cc_start: 0.0568 (tmm) cc_final: 0.0103 (ttm) REVERT: H 297 MET cc_start: 0.2368 (OUTLIER) cc_final: 0.2122 (pmm) REVERT: H 323 MET cc_start: 0.4314 (tmm) cc_final: 0.3416 (ppp) REVERT: H 332 MET cc_start: 0.3419 (pp-130) cc_final: 0.0841 (ptm) REVERT: H 360 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.4266 (tmt) REVERT: H 366 MET cc_start: 0.4333 (tpt) cc_final: 0.3834 (OUTLIER) REVERT: H 462 MET cc_start: 0.7583 (ptp) cc_final: 0.7218 (mmt) REVERT: H 474 MET cc_start: 0.1390 (ppp) cc_final: 0.0588 (ppp) REVERT: H 480 MET cc_start: 0.6509 (tpt) cc_final: 0.6124 (mmt) REVERT: H 557 MET cc_start: 0.7434 (ppp) cc_final: 0.7134 (ttt) REVERT: H 572 ASN cc_start: 0.7052 (m-40) cc_final: 0.6665 (p0) REVERT: H 579 MET cc_start: 0.2475 (mmt) cc_final: 0.1052 (tpp) outliers start: 75 outliers final: 65 residues processed: 245 average time/residue: 1.2834 time to fit residues: 396.8157 Evaluate side-chains 244 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1037 ARG Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 980 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 525 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 0.9980 chunk 408 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 383 optimal weight: 50.0000 chunk 160 optimal weight: 2.9990 chunk 394 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** G 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.181860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.116277 restraints weight = 76263.739| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.34 r_work: 0.3063 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 40988 Z= 0.287 Angle : 0.633 21.989 55741 Z= 0.311 Chirality : 0.045 0.413 6437 Planarity : 0.004 0.055 7087 Dihedral : 6.136 57.851 7323 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 2.06 % Allowed : 17.67 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.14 (0.12), residues: 4815 helix: 1.82 (0.13), residues: 1709 sheet: 0.41 (0.19), residues: 733 loop : -1.37 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 477 HIS 0.006 0.001 HIS B1062 PHE 0.020 0.002 PHE A 757 TYR 0.024 0.001 TYR C1065 ARG 0.007 0.000 ARG B1037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11062.29 seconds wall clock time: 206 minutes 26.65 seconds (12386.65 seconds total)