Starting phenix.real_space_refine on Fri Feb 23 20:58:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/02_2024/7v7z_31784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/02_2024/7v7z_31784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/02_2024/7v7z_31784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/02_2024/7v7z_31784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/02_2024/7v7z_31784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/02_2024/7v7z_31784.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.048 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 198 5.16 5 C 25400 2.51 5 N 6505 2.21 5 O 7748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39851 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "D" 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: "E" 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: "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: 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: "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: "A" 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.73, per 1000 atoms: 0.47 Number of scatterers: 39851 At special positions: 0 Unit cell: (185.9, 173.8, 238.7, 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 198 16.00 O 7748 8.00 N 6505 7.00 C 25400 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.04 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.04 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 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=1, symmetry=0 Links applied BETA1-4 " 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 340 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 340 " " NAG C2005 " - " ASN C 600 " " NAG C2006 " - " ASN C 654 " " NAG D 901 " - " ASN D 322 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 279 " " NAG I 1 " - " ASN A 328 " " NAG J 1 " - " ASN A 340 " " NAG K 1 " - " ASN A 613 " " NAG L 1 " - " ASN A 706 " " NAG M 1 " - " ASN A 714 " " NAG N 1 " - " ASN A 798 " " NAG O 1 " - " ASN A1071 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 279 " " NAG T 1 " - " ASN B 328 " " NAG U 1 " - " ASN B 613 " " NAG V 1 " - " ASN B 706 " " NAG W 1 " - " ASN B 714 " " NAG X 1 " - " ASN B 798 " " NAG Y 1 " - " ASN B1071 " " NAG Z 1 " - " ASN B1095 " " NAG a 1 " - " ASN B1131 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 279 " " NAG d 1 " - " ASN C 328 " " NAG e 1 " - " ASN C 613 " " NAG f 1 " - " ASN C 706 " " NAG g 1 " - " ASN C 714 " " NAG h 1 " - " ASN C 798 " " NAG i 1 " - " ASN C1071 " " NAG j 1 " - " ASN C1095 " " NAG k 1 " - " ASN C1131 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.24 Conformation dependent library (CDL) restraints added in 6.3 seconds 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 63 sheets defined 37.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.907A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.746A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.993A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.843A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.608A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.570A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 895 through 905 removed outlier: 3.865A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.686A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.605A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 4.133A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.050A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.931A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.915A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 removed outlier: 3.986A pdb=" N ASN B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.700A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.604A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.555A pdb=" N LEU B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 895 through 904 removed outlier: 4.327A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 removed outlier: 3.681A pdb=" N VAL B 912 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 914 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.625A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.635A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.708A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1142 removed outlier: 3.681A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.154A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.858A pdb=" N LEU C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.546A pdb=" N VAL C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 407' Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.858A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.703A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.576A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.611A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.664A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.522A pdb=" N GLN C 962 " --> pdb=" O THR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.894A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.078A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.719A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.836A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.817A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.814A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 3.532A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.644A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 268 removed outlier: 4.092A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 4.047A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.796A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 4.074A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.730A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.702A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 474 through 485 removed outlier: 3.782A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.393A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.720A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.707A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 583 through 588 removed outlier: 3.749A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.653A pdb=" N PHE D 592 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.657A pdb=" N ALA E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 79 removed outlier: 4.540A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.613A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 154 removed outlier: 3.608A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.548A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.560A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'E' and resid 218 through 229 removed outlier: 3.579A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.934A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.828A pdb=" N LEU E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 267 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY E 268 " --> pdb=" O HIS E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 263 through 268' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.866A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.891A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.878A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 400 through 412 removed outlier: 4.060A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.549A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 473 through 485 removed outlier: 3.982A pdb=" N TRP E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU E 483 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 532 removed outlier: 3.583A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.598A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.937A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'F' and resid 21 through 53 removed outlier: 3.603A pdb=" N ALA F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 77 removed outlier: 4.696A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.650A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.692A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 removed outlier: 3.809A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 228 removed outlier: 3.544A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.583A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 268 removed outlier: 4.032A pdb=" N GLY F 268 " --> pdb=" O HIS F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.642A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.583A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.684A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.671A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.626A 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 474 through 485 removed outlier: 3.755A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.761A pdb=" N VAL F 506 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.593A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 4.037A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 586 removed outlier: 3.592A pdb=" N LEU F 585 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.993A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.557A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.000A pdb=" N PHE A 43 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.829A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.616A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.616A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 93 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.864A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.573A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.943A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.367A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 573 removed outlier: 3.969A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.009A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AB7, first strand: chain 'A' and resid 714 through 725 removed outlier: 7.036A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 714 through 725 Processing sheet with id=AB9, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.638A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1078 through 1080 removed outlier: 4.567A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.649A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 49 removed outlier: 7.948A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.822A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.849A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.559A pdb=" N GLY B 308 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.559A pdb=" N GLY B 308 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.697A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.802A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.203A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD5, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD6, first strand: chain 'B' and resid 651 through 656 removed outlier: 5.985A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AD8, first strand: chain 'B' and resid 714 through 719 removed outlier: 5.877A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 722 through 725 Processing sheet with id=AE1, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AE2, first strand: chain 'B' and resid 1078 through 1080 removed outlier: 4.593A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.674A pdb=" N THR C 51 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.638A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.637A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.777A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.302A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'C' and resid 536 through 540 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.103A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AF6, first strand: chain 'C' and resid 714 through 725 removed outlier: 6.951A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 714 through 725 Processing sheet with id=AF8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.700A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1078 through 1080 removed outlier: 4.360A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG2, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.632A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.556A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.937A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 132 through 133 removed outlier: 3.691A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.010A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 132 through 133 removed outlier: 4.192A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.834A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.855A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1525 hydrogen bonds defined for protein. 4269 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: 15.99 Time building geometry restraints manager: 16.46 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: 12650 1.34 - 1.46: 10122 1.46 - 1.58: 17760 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 40820 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C PRO B 983 " pdb=" N PRO B 984 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.97e+00 bond pdb=" C PRO A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.373 0.033 2.00e-02 2.50e+03 2.66e+00 ... (remaining 40815 not shown) Histogram of bond angle deviations from ideal: 94.19 - 102.16: 97 102.16 - 110.13: 7280 110.13 - 118.10: 23538 118.10 - 126.07: 23967 126.07 - 134.04: 643 Bond angle restraints: 55525 Sorted by residual: angle pdb=" N VAL C1125 " pdb=" CA VAL C1125 " pdb=" C VAL C1125 " ideal model delta sigma weight residual 113.71 108.97 4.74 9.50e-01 1.11e+00 2.49e+01 angle pdb=" N ILE E 21 " pdb=" CA ILE E 21 " pdb=" C ILE E 21 " ideal model delta sigma weight residual 112.96 108.88 4.08 1.00e+00 1.00e+00 1.67e+01 angle pdb=" C TRP D 461 " pdb=" N MET D 462 " pdb=" CA MET D 462 " ideal model delta sigma weight residual 121.14 114.72 6.42 1.75e+00 3.27e-01 1.35e+01 angle pdb=" C GLU E 375 " pdb=" N MET E 376 " pdb=" CA MET E 376 " ideal model delta sigma weight residual 121.58 114.56 7.02 1.95e+00 2.63e-01 1.29e+01 angle pdb=" C ASN B 234 " pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 120.49 125.44 -4.95 1.38e+00 5.25e-01 1.29e+01 ... (remaining 55520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 23488 23.25 - 46.50: 1484 46.50 - 69.75: 167 69.75 - 93.01: 63 93.01 - 116.26: 22 Dihedral angle restraints: 25224 sinusoidal: 10971 harmonic: 14253 Sorted by residual: dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -174.81 88.81 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -0.88 -85.12 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 659 " pdb=" SG CYS C 659 " pdb=" SG CYS C 668 " pdb=" CB CYS C 668 " ideal model delta sinusoidal sigma weight residual -86.00 -170.58 84.58 1 1.00e+01 1.00e-02 8.69e+01 ... (remaining 25221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 6328 0.175 - 0.351: 12 0.351 - 0.526: 5 0.526 - 0.701: 1 0.701 - 0.877: 1 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG C2006 " pdb=" ND2 ASN C 654 " pdb=" C2 NAG C2006 " pdb=" O5 NAG C2006 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.57e+00 ... (remaining 6344 not shown) Planarity restraints: 7126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.024 2.00e-02 2.50e+03 2.32e-02 6.71e+00 pdb=" CG ASN A 165 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 517 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.34e+00 pdb=" N PRO A 518 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " -0.021 2.00e-02 2.50e+03 1.98e-02 4.88e+00 pdb=" CG ASN B1071 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.021 2.00e-02 2.50e+03 ... (remaining 7123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 844 2.68 - 3.23: 38788 3.23 - 3.79: 60712 3.79 - 4.34: 78181 4.34 - 4.90: 129112 Nonbonded interactions: 307637 Sorted by model distance: nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR A 713 " pdb=" O GLN A1068 " model vdw 2.153 2.440 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.166 2.440 nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.172 2.440 nonbonded pdb=" OG1 THR A 497 " pdb=" OH TYR D 41 " model vdw 2.173 2.440 ... (remaining 307632 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 1143 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 1143 or resid 2001 through 2004)) } ncs_group { reference = (chain 'D' and resid 19 through 614) selection = chain 'E' selection = chain 'F' } ncs_group { reference = 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' 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' } 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: 3.600 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: 0.040 Extract box with map and model: 14.410 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 96.340 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.720 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40820 Z= 0.230 Angle : 0.613 8.171 55525 Z= 0.319 Chirality : 0.048 0.877 6347 Planarity : 0.004 0.058 7078 Dihedral : 14.823 116.256 15912 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4830 helix: 0.96 (0.14), residues: 1566 sheet: -1.16 (0.19), residues: 681 loop : -1.62 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 165 HIS 0.006 0.001 HIS D 374 PHE 0.022 0.001 PHE A 903 TYR 0.017 0.001 TYR A1064 ARG 0.002 0.000 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 5.056 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8077 (p90) cc_final: 0.7591 (p90) REVERT: A 153 MET cc_start: 0.5655 (ppp) cc_final: 0.2988 (mmp) REVERT: A 168 PHE cc_start: 0.8132 (t80) cc_final: 0.7829 (t80) REVERT: A 239 GLN cc_start: 0.6088 (tt0) cc_final: 0.5860 (tt0) REVERT: B 52 GLN cc_start: 0.8096 (pp30) cc_final: 0.7735 (pp30) REVERT: B 160 TYR cc_start: 0.8257 (p90) cc_final: 0.8030 (p90) REVERT: C 694 MET cc_start: 0.7637 (mpp) cc_final: 0.7278 (mtp) REVERT: D 455 MET cc_start: 0.4613 (ppp) cc_final: 0.4002 (ppp) REVERT: D 462 MET cc_start: 0.6857 (pmm) cc_final: 0.5256 (mmp) REVERT: D 468 ILE cc_start: 0.0982 (pt) cc_final: -0.1034 (tp) REVERT: D 480 MET cc_start: 0.3727 (tmm) cc_final: 0.3184 (tmm) REVERT: D 579 MET cc_start: -0.1830 (tpt) cc_final: -0.2342 (tpp) REVERT: D 600 LYS cc_start: 0.3358 (mmtm) cc_final: 0.3011 (tmtt) REVERT: E 89 GLN cc_start: 0.4435 (mp10) cc_final: 0.3956 (mm110) REVERT: E 557 MET cc_start: 0.2278 (tmm) cc_final: 0.1696 (ttp) REVERT: E 579 MET cc_start: -0.2554 (mmm) cc_final: -0.3003 (ttt) REVERT: F 62 MET cc_start: 0.2853 (mmm) cc_final: 0.2544 (mmm) REVERT: F 123 MET cc_start: -0.0284 (tmm) cc_final: -0.1139 (mmm) REVERT: F 323 MET cc_start: -0.3144 (tpt) cc_final: -0.3428 (tpt) REVERT: F 383 MET cc_start: -0.0931 (tpp) cc_final: -0.1476 (ttm) REVERT: F 408 MET cc_start: -0.0962 (ptt) cc_final: -0.2561 (ttt) REVERT: F 455 MET cc_start: 0.1697 (ppp) cc_final: 0.1378 (ppp) REVERT: F 474 MET cc_start: -0.1686 (mmp) cc_final: -0.3057 (tpp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.4713 time to fit residues: 204.8646 Evaluate side-chains 173 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 30.0000 chunk 368 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 231 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 441 optimal weight: 50.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 GLN A 898 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN C 87 ASN C 898 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 40820 Z= 0.312 Angle : 0.614 8.575 55525 Z= 0.307 Chirality : 0.047 0.569 6347 Planarity : 0.004 0.050 7078 Dihedral : 9.285 106.223 6900 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.44 % Allowed : 6.55 % Favored : 93.01 % 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: -0.91 (0.12), residues: 4830 helix: 1.13 (0.13), residues: 1611 sheet: -1.22 (0.18), residues: 730 loop : -1.61 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 461 HIS 0.012 0.001 HIS D 228 PHE 0.031 0.002 PHE B1118 TYR 0.027 0.001 TYR A1064 ARG 0.009 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 4.506 Fit side-chains REVERT: A 140 PHE cc_start: 0.8086 (p90) cc_final: 0.7567 (p90) REVERT: A 153 MET cc_start: 0.5564 (ppp) cc_final: 0.3018 (mmp) REVERT: A 239 GLN cc_start: 0.6219 (tt0) cc_final: 0.5968 (tt0) REVERT: A 362 TYR cc_start: 0.8955 (m-80) cc_final: 0.8674 (m-80) REVERT: A 422 LEU cc_start: 0.9205 (tt) cc_final: 0.8949 (pp) REVERT: A 505 TYR cc_start: 0.7769 (m-10) cc_final: 0.7542 (m-10) REVERT: B 52 GLN cc_start: 0.8025 (pp30) cc_final: 0.7390 (pp30) REVERT: B 160 TYR cc_start: 0.8238 (p90) cc_final: 0.8004 (p90) REVERT: B 200 TYR cc_start: 0.7672 (m-80) cc_final: 0.7258 (m-80) REVERT: D 408 MET cc_start: 0.4157 (tpp) cc_final: 0.3686 (tpp) REVERT: D 455 MET cc_start: 0.4669 (ppp) cc_final: 0.3966 (ppp) REVERT: D 462 MET cc_start: 0.6890 (pmm) cc_final: 0.5499 (mmp) REVERT: D 468 ILE cc_start: 0.1092 (pt) cc_final: -0.0923 (tp) REVERT: D 480 MET cc_start: 0.3711 (tmm) cc_final: 0.3191 (tmm) REVERT: D 600 LYS cc_start: 0.3366 (mmtm) cc_final: 0.3042 (tmtt) REVERT: E 89 GLN cc_start: 0.4593 (mp10) cc_final: 0.3988 (mm110) REVERT: E 557 MET cc_start: 0.2274 (tmm) cc_final: 0.1727 (ttp) REVERT: E 579 MET cc_start: -0.2682 (mmm) cc_final: -0.3160 (ttt) REVERT: F 62 MET cc_start: 0.2657 (mmm) cc_final: 0.2369 (mmm) REVERT: F 123 MET cc_start: 0.0009 (tmm) cc_final: -0.0873 (mmm) REVERT: F 383 MET cc_start: -0.0718 (tpp) cc_final: -0.1357 (ttm) REVERT: F 408 MET cc_start: -0.1287 (ptt) cc_final: -0.3069 (ttt) REVERT: F 474 MET cc_start: -0.1866 (mmp) cc_final: -0.3015 (tpp) outliers start: 19 outliers final: 15 residues processed: 200 average time/residue: 0.4626 time to fit residues: 164.1223 Evaluate side-chains 184 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 50.0000 chunk 136 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 442 optimal weight: 50.0000 chunk 477 optimal weight: 2.9990 chunk 393 optimal weight: 20.0000 chunk 438 optimal weight: 0.0770 chunk 150 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 40820 Z= 0.402 Angle : 0.643 8.864 55525 Z= 0.324 Chirality : 0.048 0.499 6347 Planarity : 0.004 0.087 7078 Dihedral : 9.089 108.022 6900 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.57 % Allowed : 10.45 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 4830 helix: 1.03 (0.13), residues: 1609 sheet: -1.31 (0.19), residues: 708 loop : -1.76 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 461 HIS 0.007 0.001 HIS B1055 PHE 0.035 0.002 PHE B1118 TYR 0.031 0.002 TYR B 204 ARG 0.014 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 175 time to evaluate : 4.906 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8092 (p90) cc_final: 0.7587 (p90) REVERT: A 153 MET cc_start: 0.5604 (ppp) cc_final: 0.3061 (mmp) REVERT: A 203 ILE cc_start: 0.8014 (mt) cc_final: 0.7750 (mt) REVERT: A 204 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: A 239 GLN cc_start: 0.6226 (tt0) cc_final: 0.5998 (tt0) REVERT: A 339 PHE cc_start: 0.8259 (m-80) cc_final: 0.8021 (m-80) REVERT: A 362 TYR cc_start: 0.8968 (m-80) cc_final: 0.8275 (m-80) REVERT: A 422 LEU cc_start: 0.9220 (tt) cc_final: 0.8948 (pp) REVERT: A 505 TYR cc_start: 0.7781 (m-10) cc_final: 0.7559 (m-10) REVERT: A 764 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8406 (mm) REVERT: B 52 GLN cc_start: 0.8003 (pp30) cc_final: 0.7665 (pp30) REVERT: B 160 TYR cc_start: 0.8184 (p90) cc_final: 0.7915 (p90) REVERT: C 1086 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: D 455 MET cc_start: 0.4436 (ppp) cc_final: 0.3754 (ppp) REVERT: D 462 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.5600 (mmt) REVERT: D 480 MET cc_start: 0.3950 (tmm) cc_final: 0.3349 (tmm) REVERT: D 600 LYS cc_start: 0.3585 (mmtm) cc_final: 0.3260 (tmtt) REVERT: E 89 GLN cc_start: 0.4588 (mp10) cc_final: 0.4043 (mm110) REVERT: E 557 MET cc_start: 0.2368 (tmm) cc_final: 0.1842 (ttp) REVERT: E 579 MET cc_start: -0.2632 (mmm) cc_final: -0.3171 (ttt) REVERT: F 408 MET cc_start: -0.1248 (ptt) cc_final: -0.3036 (ttt) REVERT: F 474 MET cc_start: -0.1733 (mmp) cc_final: -0.2843 (tpp) outliers start: 67 outliers final: 46 residues processed: 230 average time/residue: 0.4714 time to fit residues: 192.6102 Evaluate side-chains 220 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 436 optimal weight: 8.9990 chunk 332 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 443 optimal weight: 30.0000 chunk 469 optimal weight: 50.0000 chunk 231 optimal weight: 2.9990 chunk 420 optimal weight: 0.0970 chunk 126 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 641 GLN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 641 GLN C 950 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40820 Z= 0.156 Angle : 0.527 8.897 55525 Z= 0.262 Chirality : 0.044 0.489 6347 Planarity : 0.004 0.049 7078 Dihedral : 8.346 106.187 6900 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.19 % Allowed : 12.20 % Favored : 86.61 % 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: -0.75 (0.12), residues: 4830 helix: 1.40 (0.13), residues: 1587 sheet: -1.12 (0.19), residues: 666 loop : -1.61 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 461 HIS 0.004 0.001 HIS D 417 PHE 0.020 0.001 PHE B 238 TYR 0.019 0.001 TYR A1064 ARG 0.004 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 4.186 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8094 (p90) cc_final: 0.7584 (p90) REVERT: A 153 MET cc_start: 0.5734 (ppp) cc_final: 0.3235 (mmp) REVERT: A 339 PHE cc_start: 0.8349 (m-80) cc_final: 0.8131 (m-80) REVERT: A 362 TYR cc_start: 0.8986 (m-80) cc_final: 0.8349 (m-80) REVERT: A 422 LEU cc_start: 0.9214 (tt) cc_final: 0.8851 (pp) REVERT: A 505 TYR cc_start: 0.7830 (m-10) cc_final: 0.7588 (m-10) REVERT: B 52 GLN cc_start: 0.7835 (pp30) cc_final: 0.7575 (pp30) REVERT: B 160 TYR cc_start: 0.8203 (p90) cc_final: 0.7967 (p90) REVERT: B 200 TYR cc_start: 0.7679 (m-80) cc_final: 0.7269 (m-80) REVERT: D 190 MET cc_start: 0.6092 (ptm) cc_final: 0.5511 (tmm) REVERT: D 408 MET cc_start: 0.4395 (tpp) cc_final: 0.3879 (tpp) REVERT: D 455 MET cc_start: 0.4562 (ppp) cc_final: 0.3918 (ppp) REVERT: D 462 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.5505 (mmt) REVERT: D 480 MET cc_start: 0.3847 (tmm) cc_final: 0.3247 (tmm) REVERT: D 600 LYS cc_start: 0.3528 (mmtm) cc_final: 0.3206 (tmtt) REVERT: E 89 GLN cc_start: 0.4463 (mp10) cc_final: 0.3992 (mm110) REVERT: E 557 MET cc_start: 0.2275 (tmm) cc_final: 0.1801 (ttp) REVERT: E 579 MET cc_start: -0.2671 (mmm) cc_final: -0.3167 (ttt) REVERT: F 62 MET cc_start: 0.2137 (mmm) cc_final: 0.1755 (mmm) REVERT: F 123 MET cc_start: -0.1674 (tmm) cc_final: -0.2124 (mmt) REVERT: F 249 MET cc_start: 0.0796 (mpp) cc_final: -0.1293 (tpp) REVERT: F 408 MET cc_start: -0.1067 (ptt) cc_final: -0.2823 (ttt) REVERT: F 474 MET cc_start: -0.1705 (mmp) cc_final: -0.2813 (tpp) outliers start: 51 outliers final: 29 residues processed: 227 average time/residue: 0.4780 time to fit residues: 189.4534 Evaluate side-chains 201 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 50.0000 chunk 266 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 400 optimal weight: 40.0000 chunk 324 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 239 optimal weight: 50.0000 chunk 421 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 484 ASN A 541 ASN A 641 GLN A 916 ASN A 932 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 HIS B 239 GLN B 910 GLN C 950 ASN C1045 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN E 51 ASN E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.168 40820 Z= 0.636 Angle : 0.768 12.604 55525 Z= 0.388 Chirality : 0.053 0.468 6347 Planarity : 0.005 0.066 7078 Dihedral : 8.907 107.981 6900 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.49 % Favored : 91.49 % Rotamer: Outliers : 2.64 % Allowed : 13.58 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4830 helix: 0.95 (0.13), residues: 1580 sheet: -1.57 (0.19), residues: 724 loop : -1.90 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 883 HIS 0.012 0.001 HIS B1055 PHE 0.045 0.003 PHE B1118 TYR 0.046 0.002 TYR B 204 ARG 0.015 0.001 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 170 time to evaluate : 4.294 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8115 (p90) cc_final: 0.7597 (p90) REVERT: A 153 MET cc_start: 0.5469 (ppp) cc_final: 0.2874 (mmp) REVERT: A 203 ILE cc_start: 0.8057 (mt) cc_final: 0.7805 (mt) REVERT: A 204 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: A 339 PHE cc_start: 0.8370 (m-80) cc_final: 0.8134 (m-80) REVERT: A 362 TYR cc_start: 0.8984 (m-80) cc_final: 0.8321 (m-80) REVERT: A 422 LEU cc_start: 0.9129 (tt) cc_final: 0.8842 (pp) REVERT: A 505 TYR cc_start: 0.7809 (m-10) cc_final: 0.7586 (m-10) REVERT: A 560 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: A 764 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 956 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8792 (mm) REVERT: B 52 GLN cc_start: 0.8075 (pp30) cc_final: 0.7648 (pp30) REVERT: B 160 TYR cc_start: 0.8064 (p90) cc_final: 0.7768 (p90) REVERT: B 737 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.8022 (mmt) REVERT: B 764 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8531 (mm) REVERT: C 204 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: C 560 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.5646 (mt0) REVERT: C 1086 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: D 82 MET cc_start: 0.6780 (ptp) cc_final: 0.6370 (pmm) REVERT: D 408 MET cc_start: 0.4558 (tpp) cc_final: 0.4001 (tpp) REVERT: D 455 MET cc_start: 0.4553 (ppp) cc_final: 0.3830 (ppp) REVERT: D 462 MET cc_start: 0.6729 (pmm) cc_final: 0.5457 (mmt) REVERT: D 480 MET cc_start: 0.4010 (tmm) cc_final: 0.3421 (tmm) REVERT: D 600 LYS cc_start: 0.3608 (mmtm) cc_final: 0.3277 (tmtt) REVERT: E 89 GLN cc_start: 0.4456 (mp10) cc_final: 0.3954 (mm-40) REVERT: E 557 MET cc_start: 0.2325 (tmm) cc_final: 0.1865 (ttp) REVERT: E 579 MET cc_start: -0.2828 (mmm) cc_final: -0.3300 (ttt) REVERT: F 62 MET cc_start: 0.2057 (mmm) cc_final: 0.1669 (mmm) REVERT: F 123 MET cc_start: -0.1558 (tmm) cc_final: -0.1933 (mmt) REVERT: F 408 MET cc_start: -0.1074 (ptt) cc_final: -0.2842 (ttt) REVERT: F 474 MET cc_start: -0.1605 (mmp) cc_final: -0.2659 (tpp) outliers start: 113 outliers final: 79 residues processed: 271 average time/residue: 0.4320 time to fit residues: 209.2204 Evaluate side-chains 252 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 164 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 158 optimal weight: 0.7980 chunk 423 optimal weight: 40.0000 chunk 92 optimal weight: 0.7980 chunk 275 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 470 optimal weight: 30.0000 chunk 390 optimal weight: 50.0000 chunk 217 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 155 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 GLN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40820 Z= 0.188 Angle : 0.559 9.569 55525 Z= 0.278 Chirality : 0.044 0.465 6347 Planarity : 0.004 0.063 7078 Dihedral : 8.251 106.775 6900 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.75 % Allowed : 14.89 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4830 helix: 1.31 (0.13), residues: 1586 sheet: -1.26 (0.20), residues: 647 loop : -1.72 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.004 0.001 HIS D 374 PHE 0.023 0.001 PHE B 238 TYR 0.022 0.001 TYR B1064 ARG 0.004 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 173 time to evaluate : 4.143 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8111 (p90) cc_final: 0.7592 (p90) REVERT: A 153 MET cc_start: 0.5810 (ppp) cc_final: 0.3209 (mmp) REVERT: A 339 PHE cc_start: 0.8373 (m-80) cc_final: 0.8163 (m-80) REVERT: A 362 TYR cc_start: 0.8931 (m-80) cc_final: 0.8644 (m-80) REVERT: A 505 TYR cc_start: 0.7745 (m-10) cc_final: 0.7501 (m-10) REVERT: A 560 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.5551 (mp10) REVERT: A 899 MET cc_start: 0.7437 (mmt) cc_final: 0.7186 (tpt) REVERT: B 52 GLN cc_start: 0.7945 (pp30) cc_final: 0.7421 (pp30) REVERT: B 160 TYR cc_start: 0.7965 (p90) cc_final: 0.7698 (p90) REVERT: B 200 TYR cc_start: 0.7750 (m-80) cc_final: 0.7380 (m-80) REVERT: D 82 MET cc_start: 0.6617 (ptp) cc_final: 0.6336 (pmm) REVERT: D 408 MET cc_start: 0.4570 (tpp) cc_final: 0.4020 (tpp) REVERT: D 455 MET cc_start: 0.4546 (ppp) cc_final: 0.3895 (ppp) REVERT: D 462 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.5455 (mmt) REVERT: D 480 MET cc_start: 0.3946 (tmm) cc_final: 0.3365 (tmm) REVERT: E 89 GLN cc_start: 0.4295 (mp10) cc_final: 0.3847 (mm-40) REVERT: E 152 MET cc_start: -0.2937 (OUTLIER) cc_final: -0.3168 (ttp) REVERT: E 557 MET cc_start: 0.2355 (tmm) cc_final: 0.1895 (ttp) REVERT: E 579 MET cc_start: -0.2815 (mmm) cc_final: -0.3310 (ttt) REVERT: F 62 MET cc_start: 0.2085 (mmm) cc_final: 0.1668 (mmm) REVERT: F 132 VAL cc_start: -0.2997 (OUTLIER) cc_final: -0.3278 (t) REVERT: F 249 MET cc_start: 0.1273 (mpp) cc_final: -0.1167 (tpp) REVERT: F 323 MET cc_start: -0.3399 (tpt) cc_final: -0.3646 (tpt) REVERT: F 408 MET cc_start: -0.1288 (ptt) cc_final: -0.3067 (ttp) REVERT: F 474 MET cc_start: -0.1536 (mmp) cc_final: -0.2668 (tpp) outliers start: 75 outliers final: 51 residues processed: 236 average time/residue: 0.4635 time to fit residues: 193.6878 Evaluate side-chains 226 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 453 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 343 optimal weight: 40.0000 chunk 266 optimal weight: 2.9990 chunk 395 optimal weight: 40.0000 chunk 262 optimal weight: 5.9990 chunk 468 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 216 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 GLN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN F 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 40820 Z= 0.460 Angle : 0.668 10.219 55525 Z= 0.335 Chirality : 0.049 0.456 6347 Planarity : 0.004 0.058 7078 Dihedral : 8.398 107.510 6900 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.50 % Allowed : 15.05 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4830 helix: 1.15 (0.13), residues: 1580 sheet: -1.46 (0.19), residues: 680 loop : -1.83 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.008 0.001 HIS B1055 PHE 0.037 0.002 PHE A1118 TYR 0.031 0.002 TYR B 204 ARG 0.009 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 169 time to evaluate : 4.187 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8115 (p90) cc_final: 0.7608 (p90) REVERT: A 153 MET cc_start: 0.5598 (ppp) cc_final: 0.3069 (mmp) REVERT: A 204 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: A 339 PHE cc_start: 0.8375 (m-80) cc_final: 0.8170 (m-80) REVERT: A 362 TYR cc_start: 0.8942 (m-80) cc_final: 0.8315 (m-80) REVERT: A 505 TYR cc_start: 0.7781 (m-10) cc_final: 0.7548 (m-10) REVERT: A 560 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.5555 (mp10) REVERT: A 956 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8781 (mm) REVERT: A 1010 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 52 GLN cc_start: 0.7879 (pp30) cc_final: 0.7393 (pp30) REVERT: B 160 TYR cc_start: 0.7923 (p90) cc_final: 0.7668 (p90) REVERT: C 263 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: C 560 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.5512 (mt0) REVERT: C 1141 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 82 MET cc_start: 0.6717 (ptp) cc_final: 0.6344 (pmm) REVERT: D 408 MET cc_start: 0.4600 (tpp) cc_final: 0.4060 (tpp) REVERT: D 455 MET cc_start: 0.4653 (ppp) cc_final: 0.4021 (ppp) REVERT: D 462 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5191 (mmt) REVERT: D 480 MET cc_start: 0.3992 (tmm) cc_final: 0.3731 (tmm) REVERT: D 557 MET cc_start: 0.7559 (tmm) cc_final: 0.7305 (tmm) REVERT: E 89 GLN cc_start: 0.4233 (mp10) cc_final: 0.3737 (mm-40) REVERT: E 152 MET cc_start: -0.2902 (OUTLIER) cc_final: -0.3137 (ttp) REVERT: E 557 MET cc_start: 0.2439 (tmm) cc_final: 0.1835 (ttp) REVERT: E 579 MET cc_start: -0.3068 (mmm) cc_final: -0.3512 (ttt) REVERT: F 62 MET cc_start: 0.2085 (mmm) cc_final: 0.1659 (mmm) REVERT: F 132 VAL cc_start: -0.3041 (OUTLIER) cc_final: -0.3306 (t) REVERT: F 408 MET cc_start: -0.1168 (ptt) cc_final: -0.3008 (ttp) REVERT: F 474 MET cc_start: -0.1515 (mmp) cc_final: -0.2586 (tpp) outliers start: 107 outliers final: 78 residues processed: 263 average time/residue: 0.4387 time to fit residues: 206.3250 Evaluate side-chains 252 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 165 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1094 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 378 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 289 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 279 optimal weight: 0.9990 chunk 141 optimal weight: 40.0000 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 319 optimal weight: 0.0470 chunk 231 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 368 optimal weight: 9.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 641 GLN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40820 Z= 0.161 Angle : 0.548 10.449 55525 Z= 0.271 Chirality : 0.044 0.448 6347 Planarity : 0.004 0.060 7078 Dihedral : 7.824 105.151 6900 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.87 % Allowed : 15.97 % Favored : 82.16 % 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: -0.80 (0.12), residues: 4830 helix: 1.40 (0.13), residues: 1593 sheet: -1.26 (0.19), residues: 678 loop : -1.64 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.021 0.001 HIS F 378 PHE 0.032 0.001 PHE D 274 TYR 0.023 0.001 TYR B1064 ARG 0.004 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 175 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8123 (p90) cc_final: 0.7606 (p90) REVERT: A 153 MET cc_start: 0.5905 (ppp) cc_final: 0.3429 (mmp) REVERT: A 339 PHE cc_start: 0.8368 (m-80) cc_final: 0.8161 (m-80) REVERT: A 362 TYR cc_start: 0.8940 (m-80) cc_final: 0.8660 (m-80) REVERT: A 505 TYR cc_start: 0.7726 (m-10) cc_final: 0.7476 (m-10) REVERT: A 560 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.5588 (mp10) REVERT: A 899 MET cc_start: 0.7408 (mmt) cc_final: 0.7134 (tpt) REVERT: B 52 GLN cc_start: 0.7770 (pp30) cc_final: 0.7349 (pp30) REVERT: B 160 TYR cc_start: 0.7894 (p90) cc_final: 0.7648 (p90) REVERT: B 200 TYR cc_start: 0.7732 (m-80) cc_final: 0.7377 (m-80) REVERT: D 82 MET cc_start: 0.6841 (ptp) cc_final: 0.6506 (pmm) REVERT: D 408 MET cc_start: 0.4617 (tpp) cc_final: 0.4054 (tpp) REVERT: D 455 MET cc_start: 0.4559 (ppp) cc_final: 0.3936 (ppp) REVERT: D 462 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5191 (mmt) REVERT: D 480 MET cc_start: 0.3949 (tmm) cc_final: 0.3686 (tmm) REVERT: E 89 GLN cc_start: 0.4291 (mp10) cc_final: 0.3792 (mm-40) REVERT: E 152 MET cc_start: -0.3133 (OUTLIER) cc_final: -0.3376 (ttp) REVERT: E 557 MET cc_start: 0.2424 (tmm) cc_final: 0.1792 (ttp) REVERT: E 579 MET cc_start: -0.3064 (mmm) cc_final: -0.3525 (ttt) REVERT: F 62 MET cc_start: 0.2218 (mmm) cc_final: 0.1799 (mmm) REVERT: F 132 VAL cc_start: -0.3010 (OUTLIER) cc_final: -0.3275 (t) REVERT: F 408 MET cc_start: -0.1078 (ptt) cc_final: -0.2843 (ttp) REVERT: F 474 MET cc_start: -0.1456 (mmp) cc_final: -0.2533 (tpp) outliers start: 80 outliers final: 61 residues processed: 243 average time/residue: 0.4438 time to fit residues: 191.9672 Evaluate side-chains 234 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 169 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 378 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 426 optimal weight: 50.0000 chunk 448 optimal weight: 20.0000 chunk 409 optimal weight: 30.0000 chunk 436 optimal weight: 30.0000 chunk 262 optimal weight: 0.0040 chunk 190 optimal weight: 2.9990 chunk 342 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 434 optimal weight: 10.0000 overall best weight: 6.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 561 GLN A 641 GLN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN F 378 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.186 40820 Z= 0.779 Angle : 0.868 14.881 55525 Z= 0.440 Chirality : 0.057 0.615 6347 Planarity : 0.006 0.080 7078 Dihedral : 8.749 109.369 6900 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.30 % Favored : 90.62 % Rotamer: Outliers : 2.76 % Allowed : 15.94 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4830 helix: 0.80 (0.13), residues: 1586 sheet: -1.78 (0.19), residues: 729 loop : -2.02 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.011 0.002 HIS B1055 PHE 0.057 0.003 PHE B1118 TYR 0.041 0.003 TYR B 204 ARG 0.020 0.001 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 168 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8150 (p90) cc_final: 0.7589 (p90) REVERT: A 153 MET cc_start: 0.5567 (ppp) cc_final: 0.2971 (mmp) REVERT: A 204 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: A 339 PHE cc_start: 0.8409 (m-80) cc_final: 0.8207 (m-80) REVERT: A 362 TYR cc_start: 0.8917 (m-80) cc_final: 0.8230 (m-80) REVERT: A 560 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: A 956 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8847 (mm) REVERT: A 1010 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8244 (mm) REVERT: B 52 GLN cc_start: 0.8052 (pp30) cc_final: 0.7550 (pp30) REVERT: B 160 TYR cc_start: 0.7978 (p90) cc_final: 0.7644 (p90) REVERT: B 263 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: B 1036 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8292 (mtp180) REVERT: C 263 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: C 560 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.5485 (mt0) REVERT: C 1141 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7944 (mt-10) REVERT: D 332 MET cc_start: 0.4538 (tmm) cc_final: 0.3859 (tmm) REVERT: D 408 MET cc_start: 0.4828 (tpp) cc_final: 0.4261 (tpp) REVERT: D 455 MET cc_start: 0.4570 (ppp) cc_final: 0.4018 (ppp) REVERT: D 462 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5336 (mmt) REVERT: E 89 GLN cc_start: 0.4328 (mp10) cc_final: 0.3828 (mm-40) REVERT: E 152 MET cc_start: -0.2696 (OUTLIER) cc_final: -0.2909 (ttp) REVERT: E 427 ASP cc_start: 0.2540 (OUTLIER) cc_final: 0.2217 (p0) REVERT: E 557 MET cc_start: 0.2351 (tmm) cc_final: 0.1726 (ttp) REVERT: E 579 MET cc_start: -0.3170 (mmm) cc_final: -0.3620 (ttt) REVERT: F 62 MET cc_start: 0.1940 (mmm) cc_final: 0.1508 (mmm) REVERT: F 132 VAL cc_start: -0.2983 (OUTLIER) cc_final: -0.3259 (t) REVERT: F 408 MET cc_start: -0.1157 (ptt) cc_final: -0.2925 (ttp) REVERT: F 474 MET cc_start: -0.1881 (mmp) cc_final: -0.2693 (tpp) outliers start: 118 outliers final: 95 residues processed: 275 average time/residue: 0.4427 time to fit residues: 216.0579 Evaluate side-chains 270 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 163 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain B residue 1094 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 378 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 286 optimal weight: 0.5980 chunk 461 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 484 optimal weight: 6.9990 chunk 445 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 297 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 40820 Z= 0.293 Angle : 0.629 10.760 55525 Z= 0.313 Chirality : 0.046 0.459 6347 Planarity : 0.004 0.065 7078 Dihedral : 8.235 113.913 6900 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.36 % Allowed : 16.48 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4830 helix: 1.11 (0.13), residues: 1587 sheet: -1.51 (0.20), residues: 655 loop : -1.88 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.016 0.001 HIS F 378 PHE 0.031 0.002 PHE C1118 TYR 0.025 0.001 TYR A1064 ARG 0.005 0.000 ARG B1036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 164 time to evaluate : 4.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8142 (p90) cc_final: 0.7615 (p90) REVERT: A 153 MET cc_start: 0.5652 (ppp) cc_final: 0.3153 (mmp) REVERT: A 339 PHE cc_start: 0.8394 (m-80) cc_final: 0.8185 (m-80) REVERT: A 362 TYR cc_start: 0.8867 (m-80) cc_final: 0.8240 (m-80) REVERT: A 505 TYR cc_start: 0.7544 (m-10) cc_final: 0.7286 (m-10) REVERT: A 560 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.5380 (mt0) REVERT: A 956 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8732 (mt) REVERT: B 52 GLN cc_start: 0.7945 (pp30) cc_final: 0.7462 (pp30) REVERT: B 160 TYR cc_start: 0.7951 (p90) cc_final: 0.7632 (p90) REVERT: B 263 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: B 1036 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8317 (mtp180) REVERT: D 82 MET cc_start: 0.6554 (ptp) cc_final: 0.6135 (pmm) REVERT: D 332 MET cc_start: 0.4370 (tmm) cc_final: 0.3724 (tmm) REVERT: D 408 MET cc_start: 0.4822 (tpp) cc_final: 0.4257 (tpp) REVERT: D 455 MET cc_start: 0.4275 (ppp) cc_final: 0.3830 (ppp) REVERT: D 462 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5267 (mmt) REVERT: D 480 MET cc_start: 0.3431 (tmm) cc_final: 0.2937 (tmm) REVERT: E 89 GLN cc_start: 0.4337 (mp10) cc_final: 0.3829 (mm-40) REVERT: E 152 MET cc_start: -0.2972 (OUTLIER) cc_final: -0.3175 (ttp) REVERT: E 557 MET cc_start: 0.2390 (tmm) cc_final: 0.1764 (ttp) REVERT: E 579 MET cc_start: -0.3113 (mmm) cc_final: -0.3582 (ttt) REVERT: F 62 MET cc_start: 0.1938 (mmm) cc_final: 0.1510 (mmm) REVERT: F 132 VAL cc_start: -0.2988 (OUTLIER) cc_final: -0.3262 (t) REVERT: F 249 MET cc_start: 0.0643 (mpp) cc_final: -0.1467 (tpp) REVERT: F 408 MET cc_start: -0.1183 (ptt) cc_final: -0.2946 (ttp) REVERT: F 474 MET cc_start: -0.1806 (mmp) cc_final: -0.2637 (tpp) outliers start: 101 outliers final: 81 residues processed: 256 average time/residue: 0.4613 time to fit residues: 209.7647 Evaluate side-chains 253 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 165 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1094 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 378 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 306 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 355 optimal weight: 7.9990 chunk 56 optimal weight: 0.0980 chunk 107 optimal weight: 0.9990 chunk 386 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 396 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 641 GLN A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.210605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.151517 restraints weight = 73414.964| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 4.51 r_work: 0.3469 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40820 Z= 0.206 Angle : 0.580 10.569 55525 Z= 0.286 Chirality : 0.044 0.447 6347 Planarity : 0.004 0.058 7078 Dihedral : 7.633 115.102 6900 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.01 % Allowed : 16.81 % Favored : 81.18 % 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: -0.93 (0.12), residues: 4830 helix: 1.30 (0.13), residues: 1598 sheet: -1.38 (0.19), residues: 686 loop : -1.71 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.029 0.001 HIS F 378 PHE 0.023 0.001 PHE B 238 TYR 0.024 0.001 TYR B1064 ARG 0.004 0.000 ARG B1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8830.88 seconds wall clock time: 162 minutes 26.21 seconds (9746.21 seconds total)