Starting phenix.real_space_refine on Mon Mar 18 10:35:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4m_29725/03_2024/8g4m_29725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4m_29725/03_2024/8g4m_29725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4m_29725/03_2024/8g4m_29725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4m_29725/03_2024/8g4m_29725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4m_29725/03_2024/8g4m_29725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4m_29725/03_2024/8g4m_29725.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 135 5.16 5 C 12837 2.51 5 N 3409 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20584 Number of models: 1 Model: "" Number of chains: 61 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "G" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "0" 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: "1" 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: "2" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 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 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: "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 Time building chain proxies: 10.19, per 1000 atoms: 0.50 Number of scatterers: 20584 At special positions: 0 Unit cell: (130.31, 132.8, 144.42, 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 135 16.00 O 4203 8.00 N 3409 7.00 C 12837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 99 " - pdb=" SG CYS J 100D" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN e 4 " - " MAN e 5 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 6 " " BMA a 3 " - " MAN a 5 " " BMA o 3 " - " MAN o 5 " " BMA t 3 " - " MAN t 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG 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 o 2 " - " BMA o 3 " " 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 t 2 " - " BMA t 3 " " 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-ASN " NAG 0 1 " - " ASN I 392 " " NAG 1 1 " - " ASN I 448 " " NAG 2 1 " - " ASN I 160 " " NAG A 701 " - " ASN A 637 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 234 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG I 601 " - " ASN I 339 " " NAG I 602 " - " ASN I 355 " " NAG M 1 " - " ASN C 88 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 197 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 276 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN G 88 " " NAG b 1 " - " ASN G 133 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN G 197 " " NAG e 1 " - " ASN G 262 " " NAG f 1 " - " ASN G 276 " " NAG g 1 " - " ASN G 295 " " NAG h 1 " - " ASN G 301 " " NAG i 1 " - " ASN G 332 " " NAG j 1 " - " ASN G 363 " " NAG k 1 " - " ASN G 386 " " NAG l 1 " - " ASN G 392 " " NAG m 1 " - " ASN G 448 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN I 88 " " NAG p 1 " - " ASN I 133 " " NAG q 1 " - " ASN I 156 " " NAG r 1 " - " ASN I 197 " " NAG s 1 " - " ASN I 234 " " NAG t 1 " - " ASN I 262 " " NAG u 1 " - " ASN I 276 " " NAG v 1 " - " ASN I 295 " " NAG w 1 " - " ASN I 301 " " NAG x 1 " - " ASN I 332 " " NAG y 1 " - " ASN I 363 " " NAG z 1 " - " ASN I 386 " Time building additional restraints: 9.06 Conformation dependent library (CDL) restraints added in 3.2 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 45 sheets defined 20.5% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.882A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.542A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.616A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.675A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.771A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.532A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.560A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.592A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.839A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.618A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.736A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.713A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.577A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.632A pdb=" N ALA I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.931A pdb=" N ARG I 151 " --> pdb=" O ASP I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 354 removed outlier: 4.030A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.917A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.164A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.471A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.744A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.755A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.513A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.932A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.690A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.248A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.640A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.297A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.452A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.586A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.657A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.263A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.470A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.617A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.544A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.656A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.171A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.508A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.561A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.041A pdb=" N ARG D 38 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.279A pdb=" N TYR D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.070A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.097A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.438A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.342A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.554A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.113A pdb=" N ARG J 38 " --> pdb=" O TYR J 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.059A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.141A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2046 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: 7.19 Time building geometry restraints manager: 9.68 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: 6415 1.34 - 1.46: 5264 1.46 - 1.58: 9118 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 20977 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" C1 NAG p 2 " pdb=" O5 NAG p 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 20972 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.22: 728 107.22 - 114.30: 12881 114.30 - 121.38: 9191 121.38 - 128.45: 5468 128.45 - 135.53: 191 Bond angle restraints: 28459 Sorted by residual: angle pdb=" C2 NAG b 2 " pdb=" N2 NAG b 2 " pdb=" C7 NAG b 2 " ideal model delta sigma weight residual 124.56 135.53 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " ideal model delta sigma weight residual 110.40 115.22 -4.82 1.70e+00 3.46e-01 8.03e+00 angle pdb=" N GLY I 389 " pdb=" CA GLY I 389 " pdb=" C GLY I 389 " ideal model delta sigma weight residual 114.66 111.25 3.41 1.24e+00 6.50e-01 7.56e+00 angle pdb=" C GLY K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 angle pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " pdb=" CD1 ILE B 635 " ideal model delta sigma weight residual 113.80 119.50 -5.70 2.10e+00 2.27e-01 7.38e+00 ... (remaining 28454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12568 21.78 - 43.56: 1097 43.56 - 65.34: 302 65.34 - 87.12: 79 87.12 - 108.90: 52 Dihedral angle restraints: 14098 sinusoidal: 7105 harmonic: 6993 Sorted by residual: dihedral pdb=" CB CYS I 201 " pdb=" SG CYS I 201 " pdb=" SG CYS I 433 " pdb=" CB CYS I 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.45 62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS D 99 " pdb=" SG CYS D 99 " pdb=" SG CYS D 100D" pdb=" CB CYS D 100D" ideal model delta sinusoidal sigma weight residual 93.00 153.67 -60.67 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -139.44 53.44 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 14095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3030 0.059 - 0.119: 419 0.119 - 0.178: 66 0.178 - 0.238: 6 0.238 - 0.297: 8 Chirality restraints: 3529 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3526 not shown) Planarity restraints: 3521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 18 " -0.176 9.50e-02 1.11e+02 7.93e-02 4.15e+00 pdb=" NE ARG K 18 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG K 18 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG K 18 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG K 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 55 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" CG ASP J 55 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP J 55 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP J 55 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 635 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C ILE B 635 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE B 635 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 636 " 0.006 2.00e-02 2.50e+03 ... (remaining 3518 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 537 2.69 - 3.24: 19246 3.24 - 3.79: 31779 3.79 - 4.35: 44438 4.35 - 4.90: 74271 Nonbonded interactions: 170271 Sorted by model distance: nonbonded pdb=" N GLU K 81 " pdb=" OE1 GLU K 81 " model vdw 2.132 2.520 nonbonded pdb=" N GLU E 81 " pdb=" OE1 GLU E 81 " model vdw 2.136 2.520 nonbonded pdb=" OE1 GLN I 258 " pdb=" OG1 THR I 387 " model vdw 2.140 2.440 nonbonded pdb=" O SER G 460 " pdb=" OG1 THR G 461 " model vdw 2.161 2.440 nonbonded pdb=" O SER I 460 " pdb=" OG1 THR I 461 " model vdw 2.188 2.440 ... (remaining 170266 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 '0' selection = chain '1' selection = chain '2' selection = chain 'N' selection = chain 'P' 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 'b' selection = chain 'c' selection = chain 'd' 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 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 514 through 664 or resid 701)) selection = chain 'B' selection = (chain 'F' and (resid 514 through 664 or resid 701)) } ncs_group { reference = (chain 'C' and (resid 31 through 505 or resid 601 through 602)) selection = (chain 'G' and (resid 31 through 505 or resid 601 through 602)) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'a' selection = chain 'e' selection = chain 'o' } ncs_group { reference = chain 'Q' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.290 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 53.000 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 0.040 20977 Z= 0.274 Angle : 0.638 10.968 28459 Z= 0.277 Chirality : 0.047 0.297 3529 Planarity : 0.003 0.079 3466 Dihedral : 18.251 108.900 9471 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.43 % Allowed : 21.18 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.60 (0.18), residues: 2384 helix: 1.74 (0.29), residues: 412 sheet: 0.15 (0.19), residues: 771 loop : 0.22 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 96 HIS 0.003 0.000 HIS G 105 PHE 0.007 0.001 PHE D 100G TYR 0.012 0.001 TYR D 100E ARG 0.009 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 259 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8458 (tpp) cc_final: 0.8173 (mpp) REVERT: A 601 LYS cc_start: 0.8922 (mttm) cc_final: 0.8625 (mttp) REVERT: G 475 MET cc_start: 0.8732 (mmm) cc_final: 0.7608 (mpp) REVERT: B 655 LYS cc_start: 0.8419 (tptm) cc_final: 0.8210 (tptp) REVERT: F 599 SER cc_start: 0.9376 (t) cc_final: 0.9055 (m) REVERT: D 3 GLN cc_start: 0.8140 (mm110) cc_final: 0.7566 (mp10) REVERT: D 13 GLN cc_start: 0.8777 (mp10) cc_final: 0.8514 (tp40) REVERT: D 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7307 (t0) REVERT: D 83 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8905 (ptp-170) REVERT: D 100 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8084 (mtp85) REVERT: D 107 THR cc_start: 0.9026 (t) cc_final: 0.8788 (p) REVERT: E 5 THR cc_start: 0.9172 (m) cc_final: 0.8960 (p) REVERT: H 38 ARG cc_start: 0.8828 (ptt180) cc_final: 0.8575 (ptt-90) REVERT: H 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7890 (t0) REVERT: H 85 GLU cc_start: 0.8953 (pm20) cc_final: 0.8688 (pm20) REVERT: H 89 VAL cc_start: 0.8596 (t) cc_final: 0.8225 (p) REVERT: H 107 THR cc_start: 0.8795 (t) cc_final: 0.8449 (p) REVERT: L 24 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: L 70 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8272 (mm-30) REVERT: J 13 GLN cc_start: 0.8563 (mm110) cc_final: 0.8267 (mm110) REVERT: J 43 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8439 (mppt) REVERT: J 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7683 (t70) REVERT: K 79 GLN cc_start: 0.8369 (mt0) cc_final: 0.8148 (mt0) outliers start: 51 outliers final: 39 residues processed: 306 average time/residue: 1.3951 time to fit residues: 479.2174 Evaluate side-chains 258 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 388 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 188 ASN C 411 ASN G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20977 Z= 0.386 Angle : 0.612 9.204 28459 Z= 0.299 Chirality : 0.046 0.271 3529 Planarity : 0.003 0.034 3466 Dihedral : 12.471 95.827 5120 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.57 % Allowed : 21.13 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.67 (0.18), residues: 2384 helix: 2.30 (0.29), residues: 384 sheet: 0.15 (0.19), residues: 750 loop : 0.16 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.004 0.001 HIS C 330 PHE 0.013 0.002 PHE F 519 TYR 0.020 0.002 TYR J 100E ARG 0.005 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 237 time to evaluate : 2.347 Fit side-chains revert: symmetry clash REVERT: C 475 MET cc_start: 0.8511 (tpp) cc_final: 0.8208 (mpp) REVERT: A 601 LYS cc_start: 0.8929 (mttm) cc_final: 0.8619 (mttp) REVERT: G 475 MET cc_start: 0.8911 (mmm) cc_final: 0.7835 (mpp) REVERT: I 114 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: I 420 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9085 (mm) REVERT: F 599 SER cc_start: 0.9384 (t) cc_final: 0.9064 (p) REVERT: F 621 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: F 655 LYS cc_start: 0.7819 (tptt) cc_final: 0.7583 (ttmt) REVERT: D 3 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8272 (mm-40) REVERT: D 13 GLN cc_start: 0.8740 (mp10) cc_final: 0.8246 (mm-40) REVERT: D 72 ASP cc_start: 0.7840 (t0) cc_final: 0.7110 (t0) REVERT: D 100 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8115 (mtp85) REVERT: D 107 THR cc_start: 0.8921 (t) cc_final: 0.8686 (p) REVERT: H 85 GLU cc_start: 0.9144 (pm20) cc_final: 0.8867 (pm20) REVERT: H 108 LEU cc_start: 0.9249 (tp) cc_final: 0.9039 (tm) REVERT: L 24 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7685 (ttp80) REVERT: J 13 GLN cc_start: 0.8555 (mm110) cc_final: 0.8272 (mm110) REVERT: J 72 ASP cc_start: 0.8039 (t0) cc_final: 0.7536 (t70) REVERT: K 17 GLU cc_start: 0.8747 (pt0) cc_final: 0.8507 (pm20) REVERT: K 79 GLN cc_start: 0.8564 (mt0) cc_final: 0.8309 (mt0) REVERT: K 81 GLU cc_start: 0.8240 (pm20) cc_final: 0.8025 (pm20) outliers start: 75 outliers final: 30 residues processed: 295 average time/residue: 1.4861 time to fit residues: 489.7330 Evaluate side-chains 250 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 179 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN I 67 ASN F 656 ASN D 13 GLN H 13 GLN H 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20977 Z= 0.239 Angle : 0.551 9.485 28459 Z= 0.268 Chirality : 0.044 0.251 3529 Planarity : 0.003 0.038 3466 Dihedral : 11.075 91.372 5091 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.14 % Allowed : 22.80 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.68 (0.18), residues: 2384 helix: 2.58 (0.29), residues: 375 sheet: 0.11 (0.19), residues: 756 loop : 0.11 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 96 HIS 0.002 0.001 HIS C 330 PHE 0.011 0.001 PHE G 383 TYR 0.016 0.001 TYR J 100E ARG 0.008 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: C 475 MET cc_start: 0.8506 (tpp) cc_final: 0.8222 (mpp) REVERT: A 601 LYS cc_start: 0.8908 (mttm) cc_final: 0.8554 (mtmm) REVERT: G 475 MET cc_start: 0.8891 (mmm) cc_final: 0.7845 (mpp) REVERT: I 114 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: F 599 SER cc_start: 0.9384 (t) cc_final: 0.9089 (p) REVERT: F 601 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8858 (mtpp) REVERT: F 621 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: F 655 LYS cc_start: 0.7826 (tptt) cc_final: 0.7548 (ttpt) REVERT: D 3 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8121 (mm-40) REVERT: D 13 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8266 (mm-40) REVERT: D 72 ASP cc_start: 0.7821 (t0) cc_final: 0.7079 (t0) REVERT: D 89 VAL cc_start: 0.8957 (t) cc_final: 0.8703 (p) REVERT: D 100 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8182 (mtp85) REVERT: H 85 GLU cc_start: 0.9118 (pm20) cc_final: 0.8751 (pm20) REVERT: H 89 VAL cc_start: 0.8795 (t) cc_final: 0.8405 (p) REVERT: H 108 LEU cc_start: 0.9254 (tp) cc_final: 0.8977 (tm) REVERT: J 13 GLN cc_start: 0.8564 (mm110) cc_final: 0.8286 (mm110) REVERT: J 43 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8453 (mppt) REVERT: J 72 ASP cc_start: 0.8013 (t0) cc_final: 0.7508 (t70) REVERT: J 105 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8856 (mm-40) REVERT: K 79 GLN cc_start: 0.8582 (mt0) cc_final: 0.8283 (mt0) REVERT: K 81 GLU cc_start: 0.8222 (pm20) cc_final: 0.8021 (pm20) outliers start: 66 outliers final: 27 residues processed: 281 average time/residue: 1.4858 time to fit residues: 467.0265 Evaluate side-chains 246 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 0.1980 chunk 229 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 80 ASN G 114 GLN F 656 ASN E 79 GLN H 13 GLN H 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20977 Z= 0.222 Angle : 0.547 9.535 28459 Z= 0.264 Chirality : 0.044 0.250 3529 Planarity : 0.003 0.046 3466 Dihedral : 10.065 86.539 5090 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.95 % Allowed : 23.51 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.70 (0.18), residues: 2384 helix: 2.61 (0.29), residues: 376 sheet: 0.15 (0.19), residues: 756 loop : 0.09 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 96 HIS 0.002 0.001 HIS C 330 PHE 0.011 0.001 PHE G 383 TYR 0.017 0.001 TYR H 100E ARG 0.009 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 226 time to evaluate : 2.354 Fit side-chains revert: symmetry clash REVERT: C 475 MET cc_start: 0.8483 (tpp) cc_final: 0.8147 (mpp) REVERT: A 601 LYS cc_start: 0.8949 (mttm) cc_final: 0.8597 (mtmm) REVERT: A 632 ASP cc_start: 0.9134 (t0) cc_final: 0.8823 (t0) REVERT: G 114 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: G 475 MET cc_start: 0.8865 (mmm) cc_final: 0.7844 (mpp) REVERT: F 599 SER cc_start: 0.9370 (t) cc_final: 0.9098 (p) REVERT: F 601 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8857 (mtpp) REVERT: F 621 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: F 655 LYS cc_start: 0.7866 (tptt) cc_final: 0.7582 (ttpt) REVERT: D 13 GLN cc_start: 0.8922 (mp10) cc_final: 0.8637 (tp40) REVERT: D 34 MET cc_start: 0.9047 (mmt) cc_final: 0.8778 (tpp) REVERT: D 72 ASP cc_start: 0.7814 (t0) cc_final: 0.7061 (t0) REVERT: D 89 VAL cc_start: 0.8981 (t) cc_final: 0.8743 (p) REVERT: D 100 ARG cc_start: 0.8637 (mtm-85) cc_final: 0.8218 (mtp85) REVERT: H 85 GLU cc_start: 0.9128 (pm20) cc_final: 0.8758 (pm20) REVERT: H 89 VAL cc_start: 0.8821 (t) cc_final: 0.8439 (p) REVERT: H 108 LEU cc_start: 0.9276 (tp) cc_final: 0.8978 (tm) REVERT: L 24 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7485 (ttm-80) REVERT: L 70 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7977 (mm-30) REVERT: J 13 GLN cc_start: 0.8580 (mm110) cc_final: 0.8286 (mm110) REVERT: J 43 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8430 (mppt) REVERT: J 72 ASP cc_start: 0.8000 (t0) cc_final: 0.7502 (t70) REVERT: J 105 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8893 (mm-40) outliers start: 62 outliers final: 32 residues processed: 272 average time/residue: 1.5310 time to fit residues: 464.9469 Evaluate side-chains 248 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN E 79 GLN H 13 GLN H 81 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20977 Z= 0.181 Angle : 0.532 9.516 28459 Z= 0.256 Chirality : 0.043 0.259 3529 Planarity : 0.003 0.030 3466 Dihedral : 9.268 81.356 5089 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.28 % Allowed : 24.08 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.72 (0.18), residues: 2384 helix: 2.65 (0.28), residues: 376 sheet: 0.17 (0.19), residues: 759 loop : 0.10 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.002 0.000 HIS G 352 PHE 0.011 0.001 PHE G 383 TYR 0.015 0.001 TYR J 100E ARG 0.007 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 227 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 138 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8755 (pp) REVERT: C 189 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7440 (pttm) REVERT: C 475 MET cc_start: 0.8461 (tpp) cc_final: 0.8089 (mpp) REVERT: A 601 LYS cc_start: 0.8959 (mttm) cc_final: 0.8609 (mtmm) REVERT: A 632 ASP cc_start: 0.9107 (t0) cc_final: 0.8790 (t0) REVERT: G 475 MET cc_start: 0.8813 (mmm) cc_final: 0.7790 (mpp) REVERT: F 599 SER cc_start: 0.9343 (t) cc_final: 0.9059 (p) REVERT: F 601 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8831 (mtpp) REVERT: F 621 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: F 655 LYS cc_start: 0.7883 (tptt) cc_final: 0.7625 (ttpt) REVERT: D 3 GLN cc_start: 0.8575 (tp40) cc_final: 0.8312 (mm-40) REVERT: D 12 VAL cc_start: 0.9604 (t) cc_final: 0.9350 (p) REVERT: D 34 MET cc_start: 0.9040 (mmp) cc_final: 0.8772 (tpp) REVERT: D 72 ASP cc_start: 0.7829 (t0) cc_final: 0.7074 (t0) REVERT: D 89 VAL cc_start: 0.8997 (t) cc_final: 0.8743 (p) REVERT: D 100 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8247 (mtp85) REVERT: D 100 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8534 (p90) REVERT: E 54 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8140 (ttm-80) REVERT: H 85 GLU cc_start: 0.9130 (pm20) cc_final: 0.8754 (pm20) REVERT: H 89 VAL cc_start: 0.8786 (t) cc_final: 0.8400 (p) REVERT: H 108 LEU cc_start: 0.9258 (tp) cc_final: 0.8955 (tm) REVERT: L 24 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7521 (ttm-80) REVERT: L 70 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7980 (mm-30) REVERT: J 13 GLN cc_start: 0.8591 (mm110) cc_final: 0.8297 (mm110) REVERT: J 43 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8424 (mppt) REVERT: J 72 ASP cc_start: 0.8013 (t0) cc_final: 0.7536 (t70) REVERT: J 105 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8893 (mm-40) REVERT: K 24 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7616 (mtm-85) REVERT: K 79 GLN cc_start: 0.8462 (mt0) cc_final: 0.8151 (mt0) REVERT: K 103 LYS cc_start: 0.8482 (tppp) cc_final: 0.8154 (tppp) outliers start: 69 outliers final: 31 residues processed: 276 average time/residue: 1.4616 time to fit residues: 451.5687 Evaluate side-chains 252 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN D 13 GLN H 13 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20977 Z= 0.306 Angle : 0.563 9.633 28459 Z= 0.269 Chirality : 0.044 0.267 3529 Planarity : 0.003 0.030 3466 Dihedral : 8.788 76.811 5082 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.24 % Allowed : 24.61 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.61 (0.18), residues: 2384 helix: 2.16 (0.28), residues: 403 sheet: 0.14 (0.19), residues: 750 loop : 0.09 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 103 HIS 0.002 0.001 HIS C 330 PHE 0.012 0.001 PHE G 383 TYR 0.018 0.001 TYR H 100E ARG 0.007 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 138 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8765 (pp) REVERT: C 189 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7448 (pttm) REVERT: C 475 MET cc_start: 0.8499 (tpp) cc_final: 0.8092 (mpp) REVERT: A 601 LYS cc_start: 0.8967 (mttm) cc_final: 0.8608 (mtmm) REVERT: A 632 ASP cc_start: 0.9153 (t0) cc_final: 0.8843 (t0) REVERT: G 475 MET cc_start: 0.8821 (mmm) cc_final: 0.7793 (mpp) REVERT: B 633 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8744 (mtpt) REVERT: I 114 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: F 599 SER cc_start: 0.9371 (t) cc_final: 0.9113 (p) REVERT: F 601 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8866 (mtpp) REVERT: F 621 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: F 655 LYS cc_start: 0.7887 (tptt) cc_final: 0.7630 (ttpt) REVERT: D 3 GLN cc_start: 0.8570 (tp40) cc_final: 0.8325 (mm-40) REVERT: D 12 VAL cc_start: 0.9578 (t) cc_final: 0.9339 (p) REVERT: D 34 MET cc_start: 0.9070 (mmp) cc_final: 0.8796 (tpp) REVERT: D 72 ASP cc_start: 0.7857 (t0) cc_final: 0.7092 (t0) REVERT: D 100 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8277 (mtp85) REVERT: D 105 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7440 (pp30) REVERT: E 32 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.5789 (mmtm) REVERT: E 54 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8077 (ttm-80) REVERT: H 85 GLU cc_start: 0.9114 (pm20) cc_final: 0.8728 (pm20) REVERT: H 108 LEU cc_start: 0.9252 (tp) cc_final: 0.8915 (tm) REVERT: L 24 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7578 (ttm-80) REVERT: L 70 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7984 (mm-30) REVERT: J 13 GLN cc_start: 0.8594 (mm110) cc_final: 0.8299 (mm110) REVERT: J 72 ASP cc_start: 0.8045 (t0) cc_final: 0.7555 (t70) REVERT: J 100 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8830 (p) REVERT: K 24 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7638 (mtm-85) REVERT: K 103 LYS cc_start: 0.8455 (tppp) cc_final: 0.8041 (tppp) outliers start: 68 outliers final: 40 residues processed: 267 average time/residue: 1.5279 time to fit residues: 455.7944 Evaluate side-chains 261 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN D 13 GLN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20977 Z= 0.256 Angle : 0.558 9.562 28459 Z= 0.266 Chirality : 0.044 0.271 3529 Planarity : 0.003 0.041 3466 Dihedral : 8.301 70.705 5080 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.52 % Allowed : 24.18 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.66 (0.18), residues: 2384 helix: 2.46 (0.28), residues: 385 sheet: 0.15 (0.19), residues: 750 loop : 0.08 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 96 HIS 0.002 0.001 HIS G 105 PHE 0.012 0.001 PHE G 383 TYR 0.016 0.001 TYR J 100E ARG 0.012 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 218 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 138 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8752 (pp) REVERT: C 475 MET cc_start: 0.8486 (tpp) cc_final: 0.8101 (mpp) REVERT: A 601 LYS cc_start: 0.8971 (mttm) cc_final: 0.8617 (mtmm) REVERT: A 632 ASP cc_start: 0.9126 (t0) cc_final: 0.8817 (t0) REVERT: G 475 MET cc_start: 0.8799 (mmm) cc_final: 0.7804 (mpp) REVERT: B 633 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8747 (mtpt) REVERT: I 114 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7910 (mp10) REVERT: F 599 SER cc_start: 0.9378 (t) cc_final: 0.9120 (p) REVERT: F 601 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8851 (mtpp) REVERT: F 621 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: F 655 LYS cc_start: 0.7931 (tptt) cc_final: 0.7678 (ttpt) REVERT: D 3 GLN cc_start: 0.8574 (tp40) cc_final: 0.8286 (mm-40) REVERT: D 6 GLU cc_start: 0.7547 (mp0) cc_final: 0.6748 (pm20) REVERT: D 12 VAL cc_start: 0.9570 (t) cc_final: 0.9318 (p) REVERT: D 34 MET cc_start: 0.9069 (mmp) cc_final: 0.8805 (tpp) REVERT: D 72 ASP cc_start: 0.7867 (t0) cc_final: 0.7101 (t0) REVERT: D 89 VAL cc_start: 0.9008 (t) cc_final: 0.8798 (p) REVERT: D 100 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8308 (mtp85) REVERT: E 32 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.5794 (mmtm) REVERT: E 54 ARG cc_start: 0.8562 (ttm110) cc_final: 0.8070 (ttm-80) REVERT: H 85 GLU cc_start: 0.9112 (pm20) cc_final: 0.8724 (pm20) REVERT: H 108 LEU cc_start: 0.9269 (tp) cc_final: 0.8937 (tm) REVERT: L 24 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7618 (ttm-80) REVERT: L 39 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7967 (mmtm) REVERT: L 70 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7985 (mm-30) REVERT: J 13 GLN cc_start: 0.8598 (mm110) cc_final: 0.8301 (mm110) REVERT: J 43 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8314 (mppt) REVERT: J 72 ASP cc_start: 0.8021 (t0) cc_final: 0.7531 (t70) REVERT: J 100 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8830 (p) REVERT: K 24 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7646 (mtm-85) REVERT: K 74 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8327 (p) REVERT: K 103 LYS cc_start: 0.8404 (tppp) cc_final: 0.7976 (tppp) outliers start: 74 outliers final: 34 residues processed: 269 average time/residue: 1.4751 time to fit residues: 443.6510 Evaluate side-chains 255 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN G 80 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 658 GLN F 656 ASN D 13 GLN H 13 GLN L 79 GLN J 39 GLN K 38 GLN K 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20977 Z= 0.420 Angle : 0.616 9.762 28459 Z= 0.296 Chirality : 0.046 0.267 3529 Planarity : 0.003 0.042 3466 Dihedral : 8.101 64.443 5080 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.86 % Allowed : 25.04 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.54 (0.18), residues: 2384 helix: 2.31 (0.28), residues: 389 sheet: 0.09 (0.19), residues: 744 loop : -0.00 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 103 HIS 0.003 0.001 HIS G 330 PHE 0.015 0.002 PHE G 383 TYR 0.020 0.002 TYR H 100E ARG 0.010 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 219 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: C 475 MET cc_start: 0.8546 (tpp) cc_final: 0.8125 (mpp) REVERT: A 601 LYS cc_start: 0.8991 (mttm) cc_final: 0.8691 (mttp) REVERT: A 632 ASP cc_start: 0.9146 (t0) cc_final: 0.8852 (t0) REVERT: G 475 MET cc_start: 0.8826 (mmm) cc_final: 0.7795 (mpp) REVERT: B 633 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (mtpt) REVERT: I 114 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: F 599 SER cc_start: 0.9405 (t) cc_final: 0.9115 (p) REVERT: F 621 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: F 655 LYS cc_start: 0.7920 (tptt) cc_final: 0.7659 (ttmt) REVERT: D 3 GLN cc_start: 0.8589 (tp40) cc_final: 0.8288 (mm-40) REVERT: D 12 VAL cc_start: 0.9524 (t) cc_final: 0.9282 (p) REVERT: D 34 MET cc_start: 0.9105 (mmp) cc_final: 0.8847 (tpp) REVERT: D 72 ASP cc_start: 0.7865 (t0) cc_final: 0.7107 (t0) REVERT: D 89 VAL cc_start: 0.8983 (t) cc_final: 0.8749 (p) REVERT: D 100 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8365 (mtp85) REVERT: E 32 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.5819 (mmtm) REVERT: E 54 ARG cc_start: 0.8618 (ttm110) cc_final: 0.8116 (ttm-80) REVERT: E 103 LYS cc_start: 0.8632 (tppp) cc_final: 0.8400 (tptp) REVERT: H 85 GLU cc_start: 0.9094 (pm20) cc_final: 0.8702 (pm20) REVERT: H 108 LEU cc_start: 0.9262 (tp) cc_final: 0.8928 (tm) REVERT: L 24 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7646 (ttm-80) REVERT: J 13 GLN cc_start: 0.8582 (mm110) cc_final: 0.8298 (mm110) REVERT: J 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7588 (t70) REVERT: J 100 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8826 (p) REVERT: K 24 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7653 (mtm-85) REVERT: K 103 LYS cc_start: 0.8370 (tppp) cc_final: 0.7941 (tppp) outliers start: 60 outliers final: 43 residues processed: 261 average time/residue: 1.4874 time to fit residues: 435.1105 Evaluate side-chains 261 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 65 optimal weight: 0.0770 chunk 192 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN D 13 GLN H 13 GLN L 79 GLN J 39 GLN K 38 GLN K 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20977 Z= 0.185 Angle : 0.559 9.621 28459 Z= 0.266 Chirality : 0.043 0.275 3529 Planarity : 0.003 0.057 3466 Dihedral : 7.319 56.878 5080 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.95 % Allowed : 25.84 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.64 (0.18), residues: 2384 helix: 2.49 (0.28), residues: 389 sheet: 0.13 (0.19), residues: 750 loop : 0.04 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 112 HIS 0.002 0.001 HIS J 35 PHE 0.012 0.001 PHE G 383 TYR 0.023 0.001 TYR E 49 ARG 0.013 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: C 475 MET cc_start: 0.8469 (tpp) cc_final: 0.8067 (mpp) REVERT: A 601 LYS cc_start: 0.8949 (mttm) cc_final: 0.8621 (mttp) REVERT: A 621 GLU cc_start: 0.8983 (tt0) cc_final: 0.7847 (tm-30) REVERT: A 632 ASP cc_start: 0.9101 (t0) cc_final: 0.8794 (t0) REVERT: G 475 MET cc_start: 0.8754 (mmm) cc_final: 0.7754 (mpp) REVERT: B 584 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 633 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8728 (mtpt) REVERT: I 114 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: F 599 SER cc_start: 0.9367 (t) cc_final: 0.9090 (p) REVERT: F 601 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8840 (mtpp) REVERT: F 621 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: F 655 LYS cc_start: 0.7864 (tptt) cc_final: 0.7594 (ttpt) REVERT: D 3 GLN cc_start: 0.8606 (tp40) cc_final: 0.8310 (mm-40) REVERT: D 34 MET cc_start: 0.9065 (mmp) cc_final: 0.8841 (tpp) REVERT: D 72 ASP cc_start: 0.7827 (t0) cc_final: 0.7084 (t0) REVERT: D 89 VAL cc_start: 0.8996 (t) cc_final: 0.8784 (p) REVERT: D 100 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8356 (mtp85) REVERT: E 54 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8069 (ttm-80) REVERT: E 103 LYS cc_start: 0.8685 (tppp) cc_final: 0.8467 (tptp) REVERT: H 85 GLU cc_start: 0.9114 (pm20) cc_final: 0.8724 (pm20) REVERT: H 100 THR cc_start: 0.9091 (t) cc_final: 0.8861 (t) REVERT: H 108 LEU cc_start: 0.9259 (tp) cc_final: 0.8957 (tm) REVERT: L 24 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7641 (ttm-80) REVERT: L 39 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8011 (mmtm) REVERT: L 70 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8051 (mm-30) REVERT: J 13 GLN cc_start: 0.8609 (mm110) cc_final: 0.8322 (mm110) REVERT: J 43 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8284 (mppt) REVERT: J 72 ASP cc_start: 0.8060 (t0) cc_final: 0.7568 (t70) REVERT: J 100 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8852 (p) REVERT: K 24 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7526 (mtm-85) REVERT: K 103 LYS cc_start: 0.8377 (tppp) cc_final: 0.7933 (tppp) outliers start: 41 outliers final: 29 residues processed: 249 average time/residue: 1.4899 time to fit residues: 414.4547 Evaluate side-chains 248 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 114 GLN F 656 ASN H 13 GLN L 79 GLN J 39 GLN K 38 GLN K 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20977 Z= 0.343 Angle : 0.597 9.878 28459 Z= 0.285 Chirality : 0.044 0.270 3529 Planarity : 0.003 0.041 3466 Dihedral : 7.081 56.607 5078 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.86 % Allowed : 26.37 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.58 (0.18), residues: 2384 helix: 2.40 (0.28), residues: 389 sheet: 0.13 (0.19), residues: 744 loop : -0.01 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 103 HIS 0.003 0.001 HIS G 105 PHE 0.014 0.001 PHE G 383 TYR 0.022 0.001 TYR E 49 ARG 0.011 0.000 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: C 475 MET cc_start: 0.8523 (tpp) cc_final: 0.8101 (mpp) REVERT: A 601 LYS cc_start: 0.8991 (mttm) cc_final: 0.8677 (mttp) REVERT: A 621 GLU cc_start: 0.9004 (tt0) cc_final: 0.7833 (tm-30) REVERT: A 632 ASP cc_start: 0.9156 (t0) cc_final: 0.8855 (t0) REVERT: G 475 MET cc_start: 0.8809 (mmm) cc_final: 0.7797 (mpp) REVERT: B 584 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8265 (mt-10) REVERT: B 633 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8747 (mtpt) REVERT: I 114 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: F 599 SER cc_start: 0.9390 (t) cc_final: 0.9118 (p) REVERT: F 621 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: F 655 LYS cc_start: 0.7851 (tptt) cc_final: 0.7587 (ttmt) REVERT: D 3 GLN cc_start: 0.8602 (tp40) cc_final: 0.8332 (mm-40) REVERT: D 34 MET cc_start: 0.9112 (mmp) cc_final: 0.8854 (tpp) REVERT: D 72 ASP cc_start: 0.7857 (t0) cc_final: 0.7099 (t0) REVERT: D 89 VAL cc_start: 0.9000 (t) cc_final: 0.8773 (p) REVERT: D 100 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8371 (mtp85) REVERT: E 54 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8129 (ttm-80) REVERT: E 103 LYS cc_start: 0.8664 (tppp) cc_final: 0.8446 (tptp) REVERT: H 85 GLU cc_start: 0.9100 (pm20) cc_final: 0.8712 (pm20) REVERT: H 108 LEU cc_start: 0.9251 (tp) cc_final: 0.8936 (tm) REVERT: L 24 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7566 (ttm-80) REVERT: J 13 GLN cc_start: 0.8594 (mm110) cc_final: 0.8300 (mm110) REVERT: J 43 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8280 (mppt) REVERT: J 72 ASP cc_start: 0.8079 (t0) cc_final: 0.7608 (t70) REVERT: J 100 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8844 (p) REVERT: K 24 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7599 (mtm-85) REVERT: K 103 LYS cc_start: 0.8377 (tppp) cc_final: 0.7953 (tppp) outliers start: 39 outliers final: 32 residues processed: 245 average time/residue: 1.5714 time to fit residues: 429.0273 Evaluate side-chains 249 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN H 13 GLN L 79 GLN J 39 GLN K 38 GLN K 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.051680 restraints weight = 48423.441| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.57 r_work: 0.2524 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20977 Z= 0.270 Angle : 0.574 9.567 28459 Z= 0.273 Chirality : 0.043 0.269 3529 Planarity : 0.003 0.063 3466 Dihedral : 6.727 56.677 5078 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.24 % Allowed : 25.99 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.58 (0.18), residues: 2384 helix: 2.45 (0.28), residues: 389 sheet: 0.09 (0.19), residues: 750 loop : 0.00 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 112 HIS 0.002 0.001 HIS J 35 PHE 0.012 0.001 PHE G 383 TYR 0.021 0.001 TYR E 49 ARG 0.014 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7387.32 seconds wall clock time: 132 minutes 10.33 seconds (7930.33 seconds total)