Starting phenix.real_space_refine on Tue Apr 16 17:10:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v86_31791/04_2024/7v86_31791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v86_31791/04_2024/7v86_31791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v86_31791/04_2024/7v86_31791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v86_31791/04_2024/7v86_31791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v86_31791/04_2024/7v86_31791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v86_31791/04_2024/7v86_31791.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.061 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 25476 2.51 5 N 6531 2.21 5 O 7791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 312": "OE1" <-> "OE2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39996 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "B" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 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: "F" 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: 20.40, per 1000 atoms: 0.51 Number of scatterers: 39996 At special positions: 0 Unit cell: (159.5, 177.1, 244.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 7791 8.00 N 6531 7.00 C 25476 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 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 343 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 343 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 343 " " NAG C2003 " - " ASN C 603 " " NAG C2004 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F2001 " - " ASN F 53 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 331 " " NAG L 1 " - " ASN A 616 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 165 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG W 1 " - " ASN B 331 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B1098 " " NAG d 1 " - " ASN B1134 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 165 " " NAG g 1 " - " ASN C 234 " " NAG i 1 " - " ASN C 331 " " NAG j 1 " - " ASN C 616 " " NAG k 1 " - " ASN C 709 " " NAG l 1 " - " ASN C 717 " " NAG m 1 " - " ASN C 801 " " NAG n 1 " - " ASN C1074 " " NAG o 1 " - " ASN C1098 " " NAG p 1 " - " ASN C1134 " " NAG q 1 " - " ASN F 322 " Time building additional restraints: 16.33 Conformation dependent library (CDL) restraints added in 6.8 seconds 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9186 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 52 sheets defined 38.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.928A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.354A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.807A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.183A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.745A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.526A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.703A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.412A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.951A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.349A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.989A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.292A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.592A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.879A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.515A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.558A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.651A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.579A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.633A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.471A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.768A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.355A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.713A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.704A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.601A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.673A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.888A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.682A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.908A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 175 through 194 removed outlier: 4.040A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 Processing helix chain 'F' and resid 218 through 231 removed outlier: 4.251A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 251 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.777A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.847A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.126A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.590A 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 470 through 473 removed outlier: 3.656A pdb=" N TRP F 473 " --> pdb=" O LYS F 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 470 through 473' Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.230A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.558A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 4.032A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.602A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 597 removed outlier: 4.096A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.557A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 79 removed outlier: 3.646A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TRP G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 101 removed outlier: 3.684A pdb=" N ALA G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 152 Processing helix chain 'G' and resid 157 through 171 Processing helix chain 'G' and resid 176 through 194 removed outlier: 3.683A pdb=" N VAL G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 205 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 218 through 231 removed outlier: 3.818A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 251 Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 385 Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 397 through 412 removed outlier: 4.383A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 447 removed outlier: 3.506A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 473 through 484 removed outlier: 3.550A pdb=" N TRP G 477 " --> pdb=" O TRP G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 502 Processing helix chain 'G' and resid 503 through 508 Processing helix chain 'G' and resid 512 through 532 removed outlier: 3.967A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU G 520 " --> pdb=" O TYR G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.724A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.937A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.842A pdb=" N LEU G 585 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE G 588 " --> pdb=" O LEU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.996A pdb=" N ASN G 599 " --> pdb=" O LEU G 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.508A pdb=" N GLN H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 80 removed outlier: 3.721A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 101 removed outlier: 3.721A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 157 through 171 removed outlier: 3.560A pdb=" N ARG H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.307A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 218 through 231 removed outlier: 4.017A pdb=" N LEU H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.507A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 412 removed outlier: 4.305A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.616A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.677A pdb=" N SER H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN H 508 " --> pdb=" O PHE H 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 503 through 508' Processing helix chain 'H' and resid 512 through 532 removed outlier: 4.095A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.736A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 removed outlier: 3.587A pdb=" N SER H 563 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 560 through 564' Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.719A pdb=" N LEU H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE H 588 " --> pdb=" O LEU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 599 removed outlier: 4.016A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.461A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.666A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.853A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 11.698A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.508A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.377A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.713A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.096A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.474A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.467A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.709A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.779A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.800A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 11.576A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.589A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.024A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 573 through 576 removed outlier: 3.768A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.983A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.879A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.726A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.580A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.870A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.709A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.469A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.085A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.503A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.001A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.468A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.522A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 4.826A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'G' and resid 132 through 133 Processing sheet with id=AF5, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AF6, first strand: chain 'H' and resid 132 through 133 Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 350 1680 hydrogen bonds defined for protein. 4740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.19 Time building geometry restraints manager: 17.67 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: 12713 1.34 - 1.47: 10382 1.47 - 1.59: 17576 1.59 - 1.71: 0 1.71 - 1.83: 288 Bond restraints: 40959 Sorted by residual: bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG q 2 " pdb=" O5 NAG q 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.74e+00 ... (remaining 40954 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.20: 779 105.20 - 112.40: 20953 112.40 - 119.59: 13170 119.59 - 126.79: 20216 126.79 - 133.99: 589 Bond angle restraints: 55707 Sorted by residual: angle pdb=" C ASP F 382 " pdb=" N MET F 383 " pdb=" CA MET F 383 " ideal model delta sigma weight residual 122.38 115.29 7.09 1.81e+00 3.05e-01 1.54e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 110.30 3.41 9.50e-01 1.11e+00 1.29e+01 angle pdb=" N TYR H 255 " pdb=" CA TYR H 255 " pdb=" C TYR H 255 " ideal model delta sigma weight residual 114.56 110.41 4.15 1.27e+00 6.20e-01 1.07e+01 angle pdb=" N TYR C 380 " pdb=" CA TYR C 380 " pdb=" C TYR C 380 " ideal model delta sigma weight residual 114.56 110.55 4.01 1.27e+00 6.20e-01 9.98e+00 angle pdb=" C THR H 334 " pdb=" N ASP H 335 " pdb=" CA ASP H 335 " ideal model delta sigma weight residual 121.80 129.12 -7.32 2.44e+00 1.68e-01 9.00e+00 ... (remaining 55702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 22840 17.94 - 35.88: 2098 35.88 - 53.82: 407 53.82 - 71.76: 83 71.76 - 89.70: 36 Dihedral angle restraints: 25464 sinusoidal: 11199 harmonic: 14265 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -170.40 84.40 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -163.97 77.97 1 1.00e+01 1.00e-02 7.60e+01 ... (remaining 25461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5788 0.082 - 0.163: 587 0.163 - 0.245: 18 0.245 - 0.326: 0 0.326 - 0.408: 2 Chirality restraints: 6395 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C1 NAG C2001 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C2001 " pdb=" O5 NAG C2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 6392 not shown) Planarity restraints: 7144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO C 987 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 295 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO C 295 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.029 5.00e-02 4.00e+02 ... (remaining 7141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1439 2.71 - 3.26: 40269 3.26 - 3.81: 64892 3.81 - 4.35: 77434 4.35 - 4.90: 132110 Nonbonded interactions: 316144 Sorted by model distance: nonbonded pdb=" O TYR H 215 " pdb=" OG1 THR H 567 " model vdw 2.163 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.171 2.520 nonbonded pdb=" OE2 GLU C 725 " pdb=" NE2 HIS C1064 " model vdw 2.191 2.520 nonbonded pdb=" NE1 TRP F 271 " pdb=" O SER F 502 " model vdw 2.193 2.520 nonbonded pdb=" OE1 GLN A 804 " pdb=" O6 NAG O 1 " model vdw 2.195 2.440 ... (remaining 316139 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = (chain 'F' and resid 19 through 614) selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 14.140 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 104.210 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.780 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: 0.020 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 0.063 40959 Z= 0.272 Angle : 0.600 7.894 55707 Z= 0.304 Chirality : 0.045 0.408 6395 Planarity : 0.004 0.062 7095 Dihedral : 13.942 89.704 16134 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 4827 helix: 1.42 (0.13), residues: 1694 sheet: 0.14 (0.18), residues: 781 loop : -1.40 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 886 HIS 0.006 0.001 HIS G 374 PHE 0.025 0.001 PHE B 906 TYR 0.020 0.001 TYR B 636 ARG 0.004 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8303 (pp) cc_final: 0.7914 (tp) REVERT: A 452 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7535 (ttm170) REVERT: B 66 HIS cc_start: 0.6083 (t70) cc_final: 0.4898 (p-80) REVERT: B 140 PHE cc_start: 0.6784 (p90) cc_final: 0.6407 (p90) REVERT: B 168 PHE cc_start: 0.6973 (t80) cc_final: 0.6591 (t80) REVERT: F 231 GLU cc_start: 0.7071 (mp0) cc_final: 0.6662 (mm-30) REVERT: F 323 MET cc_start: 0.3076 (tpt) cc_final: 0.2547 (mmm) REVERT: F 408 MET cc_start: 0.6422 (pmm) cc_final: 0.6204 (pmm) REVERT: G 323 MET cc_start: 0.0497 (tpt) cc_final: -0.0456 (mmm) REVERT: G 332 MET cc_start: -0.1438 (ptm) cc_final: -0.2709 (mmt) REVERT: G 366 MET cc_start: 0.1892 (mmt) cc_final: 0.1657 (mmm) REVERT: G 474 MET cc_start: 0.1317 (tpp) cc_final: -0.0412 (mmm) REVERT: H 159 ASN cc_start: 0.5187 (t0) cc_final: 0.4710 (m-40) REVERT: H 249 MET cc_start: 0.2138 (mmt) cc_final: 0.1322 (mmm) REVERT: H 270 MET cc_start: 0.2641 (ptm) cc_final: 0.2406 (ptp) REVERT: H 360 MET cc_start: -0.1591 (ttt) cc_final: -0.1815 (ttt) REVERT: H 455 MET cc_start: 0.4782 (ppp) cc_final: 0.4381 (ptt) REVERT: H 462 MET cc_start: 0.4892 (mmp) cc_final: 0.4606 (ttm) REVERT: H 582 ARG cc_start: 0.6299 (mmm-85) cc_final: 0.5805 (ttt-90) outliers start: 0 outliers final: 2 residues processed: 348 average time/residue: 1.3803 time to fit residues: 597.2423 Evaluate side-chains 182 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 950 ASP 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: 40.0000 chunk 204 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 196 optimal weight: 0.9990 chunk 380 optimal weight: 50.0000 chunk 147 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 441 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 188 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 GLN ** H 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 40959 Z= 0.347 Angle : 0.635 9.900 55707 Z= 0.322 Chirality : 0.047 0.310 6395 Planarity : 0.004 0.063 7095 Dihedral : 6.500 59.637 7072 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 1.56 % Allowed : 8.34 % Favored : 90.09 % 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: -0.29 (0.12), residues: 4827 helix: 1.37 (0.12), residues: 1711 sheet: 0.03 (0.18), residues: 773 loop : -1.51 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 886 HIS 0.008 0.001 HIS C1048 PHE 0.041 0.002 PHE C 906 TYR 0.028 0.002 TYR C1067 ARG 0.016 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 201 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8349 (pp) cc_final: 0.8080 (tp) REVERT: A 452 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7505 (tpp80) REVERT: A 934 ILE cc_start: 0.8425 (tt) cc_final: 0.8184 (mp) REVERT: A 950 ASP cc_start: 0.7555 (m-30) cc_final: 0.7258 (m-30) REVERT: B 66 HIS cc_start: 0.6380 (t70) cc_final: 0.5177 (p-80) REVERT: B 140 PHE cc_start: 0.6913 (p90) cc_final: 0.6460 (p90) REVERT: C 309 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: F 231 GLU cc_start: 0.7152 (mp0) cc_final: 0.6885 (mm-30) REVERT: F 323 MET cc_start: 0.3027 (tpt) cc_final: 0.2552 (mmm) REVERT: F 408 MET cc_start: 0.6461 (pmm) cc_final: 0.6214 (pmm) REVERT: F 510 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7648 (t80) REVERT: G 323 MET cc_start: -0.0007 (tpt) cc_final: -0.0469 (mmm) REVERT: G 332 MET cc_start: -0.1727 (ptm) cc_final: -0.2952 (mmt) REVERT: G 467 GLU cc_start: 0.2749 (mp0) cc_final: 0.2447 (pm20) REVERT: G 468 ILE cc_start: -0.1125 (OUTLIER) cc_final: -0.1708 (pp) REVERT: G 474 MET cc_start: 0.0770 (tpp) cc_final: -0.0065 (mmm) REVERT: H 159 ASN cc_start: 0.5097 (t0) cc_final: 0.4603 (m-40) REVERT: H 249 MET cc_start: 0.2023 (mmt) cc_final: 0.1196 (mmm) REVERT: H 455 MET cc_start: 0.4582 (ppp) cc_final: 0.4317 (ptt) REVERT: H 462 MET cc_start: 0.4903 (mmp) cc_final: 0.4621 (ttm) REVERT: H 582 ARG cc_start: 0.6442 (mmm-85) cc_final: 0.5929 (ttt-90) outliers start: 67 outliers final: 30 residues processed: 245 average time/residue: 1.4749 time to fit residues: 449.5783 Evaluate side-chains 204 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 510 TYR Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 608 THR Chi-restraints excluded: chain H residue 480 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 300 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 442 optimal weight: 40.0000 chunk 477 optimal weight: 20.0000 chunk 393 optimal weight: 0.7980 chunk 438 optimal weight: 0.0030 chunk 150 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1005 GLN A1088 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1002 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 ASN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40959 Z= 0.196 Angle : 0.556 9.853 55707 Z= 0.281 Chirality : 0.043 0.306 6395 Planarity : 0.004 0.059 7095 Dihedral : 6.015 59.483 7068 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 1.70 % Allowed : 11.63 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 4827 helix: 1.49 (0.13), residues: 1712 sheet: 0.17 (0.18), residues: 751 loop : -1.47 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 886 HIS 0.017 0.001 HIS A 207 PHE 0.024 0.001 PHE B 329 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 192 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7497 (tpp80) REVERT: A 855 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7182 (m-10) REVERT: A 950 ASP cc_start: 0.7563 (m-30) cc_final: 0.7277 (m-30) REVERT: B 66 HIS cc_start: 0.6301 (t70) cc_final: 0.5190 (p-80) REVERT: B 140 PHE cc_start: 0.6894 (p90) cc_final: 0.6017 (p90) REVERT: B 878 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8588 (mt) REVERT: C 309 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: F 295 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6582 (t0) REVERT: F 297 MET cc_start: -0.0031 (OUTLIER) cc_final: -0.0315 (ptt) REVERT: F 323 MET cc_start: 0.2847 (tpt) cc_final: 0.2366 (mmm) REVERT: F 408 MET cc_start: 0.6635 (pmm) cc_final: 0.6343 (pmm) REVERT: F 510 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7676 (t80) REVERT: G 323 MET cc_start: 0.0101 (tpt) cc_final: -0.0243 (mmm) REVERT: G 332 MET cc_start: -0.1590 (ptm) cc_final: -0.2853 (mmt) REVERT: G 467 GLU cc_start: 0.2732 (mp0) cc_final: 0.2415 (pm20) REVERT: G 468 ILE cc_start: -0.1238 (OUTLIER) cc_final: -0.1661 (pp) REVERT: G 474 MET cc_start: 0.0849 (tpp) cc_final: -0.0015 (mmm) REVERT: G 579 MET cc_start: -0.0163 (ttm) cc_final: -0.0443 (ptm) REVERT: H 159 ASN cc_start: 0.5143 (t0) cc_final: 0.4658 (m-40) REVERT: H 249 MET cc_start: 0.1662 (mmt) cc_final: 0.0988 (mmm) REVERT: H 462 MET cc_start: 0.4942 (mmp) cc_final: 0.4663 (ttm) REVERT: H 474 MET cc_start: -0.0262 (mtp) cc_final: -0.0555 (pmm) REVERT: H 480 MET cc_start: 0.3266 (OUTLIER) cc_final: 0.3011 (ttm) REVERT: H 579 MET cc_start: 0.1862 (tpt) cc_final: 0.1445 (tpp) REVERT: H 582 ARG cc_start: 0.6477 (mmm-85) cc_final: 0.5983 (tmt-80) outliers start: 73 outliers final: 31 residues processed: 249 average time/residue: 1.3466 time to fit residues: 424.6178 Evaluate side-chains 205 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 510 TYR Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 608 THR Chi-restraints excluded: chain H residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 436 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 443 optimal weight: 30.0000 chunk 469 optimal weight: 40.0000 chunk 231 optimal weight: 2.9990 chunk 420 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 188 ASN A 207 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 GLN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 586 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40959 Z= 0.337 Angle : 0.619 10.687 55707 Z= 0.311 Chirality : 0.046 0.337 6395 Planarity : 0.004 0.077 7095 Dihedral : 5.936 58.851 7068 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 2.56 % Allowed : 13.01 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4827 helix: 1.40 (0.13), residues: 1704 sheet: 0.01 (0.18), residues: 753 loop : -1.53 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 886 HIS 0.006 0.001 HIS C1048 PHE 0.028 0.002 PHE B 329 TYR 0.026 0.001 TYR C1067 ARG 0.009 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 178 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8400 (t80) cc_final: 0.8170 (t80) REVERT: A 452 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7519 (tpp80) REVERT: A 855 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: A 950 ASP cc_start: 0.7624 (m-30) cc_final: 0.7330 (m-30) REVERT: A 1106 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: B 66 HIS cc_start: 0.6463 (t70) cc_final: 0.5286 (p-80) REVERT: B 140 PHE cc_start: 0.6819 (p90) cc_final: 0.6217 (p90) REVERT: C 309 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: C 1039 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7876 (ptm160) REVERT: F 295 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6528 (t0) REVERT: F 323 MET cc_start: 0.3310 (tpt) cc_final: 0.2742 (mmm) REVERT: G 323 MET cc_start: 0.0219 (tpt) cc_final: -0.0199 (mmm) REVERT: G 332 MET cc_start: -0.1502 (ptm) cc_final: -0.2761 (mmt) REVERT: G 467 GLU cc_start: 0.2707 (mp0) cc_final: 0.2378 (pm20) REVERT: G 468 ILE cc_start: -0.1164 (OUTLIER) cc_final: -0.1672 (pp) REVERT: G 474 MET cc_start: 0.0846 (tpp) cc_final: -0.0014 (mmm) REVERT: H 159 ASN cc_start: 0.5142 (t0) cc_final: 0.4716 (m-40) REVERT: H 249 MET cc_start: 0.1690 (mmt) cc_final: 0.0993 (mmm) REVERT: H 462 MET cc_start: 0.4943 (mmp) cc_final: 0.4678 (ttm) REVERT: H 579 MET cc_start: 0.1868 (tpt) cc_final: 0.1436 (tpp) REVERT: H 582 ARG cc_start: 0.6411 (mmm-85) cc_final: 0.5925 (tmt-80) outliers start: 110 outliers final: 49 residues processed: 267 average time/residue: 1.3530 time to fit residues: 457.8746 Evaluate side-chains 223 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 168 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 349 optimal weight: 20.0000 chunk 193 optimal weight: 0.7980 chunk 400 optimal weight: 40.0000 chunk 324 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 239 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS F 472 GLN G 51 ASN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 210 ASN ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.125 40959 Z= 0.790 Angle : 0.854 12.442 55707 Z= 0.434 Chirality : 0.059 0.701 6395 Planarity : 0.006 0.062 7095 Dihedral : 6.726 59.595 7068 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 3.40 % Allowed : 15.15 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.12), residues: 4827 helix: 0.88 (0.12), residues: 1702 sheet: -0.52 (0.18), residues: 745 loop : -1.83 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 353 HIS 0.019 0.002 HIS A 207 PHE 0.036 0.003 PHE A1121 TYR 0.039 0.003 TYR C1067 ARG 0.023 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9654 Ramachandran restraints generated. 4827 Oldfield, 0 Emsley, 4827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 173 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8313 (t80) cc_final: 0.8088 (t80) REVERT: A 452 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7480 (tpp80) REVERT: A 560 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 855 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: A 950 ASP cc_start: 0.7782 (m-30) cc_final: 0.7456 (m-30) REVERT: A 1106 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8821 (pt0) REVERT: B 140 PHE cc_start: 0.7095 (p90) cc_final: 0.6491 (p90) REVERT: B 641 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8139 (p0) REVERT: B 869 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8703 (mtt) REVERT: B 878 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 1039 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7987 (ptm160) REVERT: C 1039 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7623 (ptm160) REVERT: F 323 MET cc_start: 0.3606 (tpt) cc_final: 0.2977 (mmm) REVERT: F 579 MET cc_start: 0.1800 (tpp) cc_final: 0.1548 (tpt) REVERT: G 82 MET cc_start: 0.3331 (OUTLIER) cc_final: 0.2974 (ppp) REVERT: G 323 MET cc_start: 0.0149 (tpt) cc_final: -0.0262 (mmm) REVERT: G 332 MET cc_start: -0.1643 (ptm) cc_final: -0.2836 (mmt) REVERT: G 462 MET cc_start: 0.4652 (ptp) cc_final: 0.4443 (ptm) REVERT: G 467 GLU cc_start: 0.2812 (mp0) cc_final: 0.2445 (pm20) REVERT: G 468 ILE cc_start: -0.1235 (OUTLIER) cc_final: -0.1686 (pp) REVERT: G 474 MET cc_start: 0.0857 (tpp) cc_final: -0.0046 (mmm) REVERT: G 491 VAL cc_start: 0.1997 (OUTLIER) cc_final: 0.1740 (t) REVERT: G 531 GLN cc_start: 0.4222 (OUTLIER) cc_final: 0.3954 (pt0) REVERT: H 159 ASN cc_start: 0.5401 (t0) cc_final: 0.4982 (m-40) REVERT: H 249 MET cc_start: 0.1965 (mmt) cc_final: 0.1181 (mmm) REVERT: H 462 MET cc_start: 0.4930 (mmp) cc_final: 0.4669 (ttm) REVERT: H 579 MET cc_start: 0.1724 (tpt) cc_final: 0.1274 (tpp) REVERT: H 582 ARG cc_start: 0.6328 (mmm-85) cc_final: 0.5821 (tmt-80) outliers start: 146 outliers final: 75 residues processed: 294 average time/residue: 1.2598 time to fit residues: 479.7760 Evaluate side-chains 253 residues out of total 4290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 166 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 491 VAL Chi-restraints excluded: chain G residue 531 GLN Chi-restraints excluded: chain G residue 608 THR Chi-restraints excluded: chain H residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 158 optimal weight: 0.0050 chunk 423 optimal weight: 30.0000 chunk 92 optimal weight: 0.8980 chunk 275 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 470 optimal weight: 20.0000 chunk 390 optimal weight: 50.0000 chunk 217 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: