Starting phenix.real_space_refine on Tue Mar 19 11:14:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3a_14474/03_2024/7z3a_14474.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3a_14474/03_2024/7z3a_14474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3a_14474/03_2024/7z3a_14474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3a_14474/03_2024/7z3a_14474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3a_14474/03_2024/7z3a_14474.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3a_14474/03_2024/7z3a_14474.pdb" } resolution = 3.95 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= 0.029 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 134 5.16 5 C 15025 2.51 5 N 3913 2.21 5 O 4928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24000 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3403 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3403 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "E" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3403 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 907 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Chain: "G" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "K" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 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: "S" 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: "T" 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: "U" 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: "V" 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: "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: 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: "Y" 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: "c" 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: "d" 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 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: "k" 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: "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: 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: "n" 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: "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: 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: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 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: "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: 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: "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: 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: "x" 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: "y" 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: "z" 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: "0" 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: "1" 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: "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: "3" 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: "4" 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: "5" 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: "6" 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: "7" 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: "8" 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: "9" 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: "AA" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 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: "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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 12.53, per 1000 atoms: 0.52 Number of scatterers: 24000 At special positions: 0 Unit cell: (135.7, 151.8, 162.15, 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 134 16.00 O 4928 8.00 N 3913 7.00 C 15025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 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 E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " 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 w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " BETA1-6 " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG 0 1 " - " ASN D 262 " " NAG 1 1 " - " ASN D 276 " " NAG 2 1 " - " ASN D 289 " " NAG 3 1 " - " ASN D 301 " " NAG 4 1 " - " ASN D 362 " " NAG 5 1 " - " ASN D 386 " " NAG 6 1 " - " ASN D 392 " " NAG 7 1 " - " ASN D 448 " " NAG 8 1 " - " ASN D 295 " " NAG 9 1 " - " ASN F 611 " " NAG A 601 " - " ASN A 156 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 396 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 156 " " NAG C 602 " - " ASN C 396 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 160 " " NAG D 603 " - " ASN D 332 " " NAG D 604 " - " ASN D 339 " " NAG D 605 " - " ASN D 130 " " NAG D 606 " - " ASN D 396 " " NAG E 701 " - " ASN E 616 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 637 " " NAG Q 1 " - " ASN A 130 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 241 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 276 " " NAG W 1 " - " ASN A 289 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 362 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN B 625 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 130 " " NAG h 1 " - " ASN C 197 " " NAG i 1 " - " ASN C 241 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 289 " " NAG m 1 " - " ASN C 295 " " NAG n 1 " - " ASN C 301 " " NAG o 1 " - " ASN C 362 " " NAG p 1 " - " ASN C 386 " " NAG q 1 " - " ASN C 392 " " NAG r 1 " - " ASN C 448 " " NAG s 1 " - " ASN C 160 " " NAG t 1 " - " ASN C 234 " " NAG u 1 " - " ASN E 611 " " NAG v 1 " - " ASN E 625 " " NAG w 1 " - " ASN D 88 " " NAG x 1 " - " ASN D 197 " " NAG y 1 " - " ASN D 234 " " NAG z 1 " - " ASN D 241 " " NAGAA 1 " - " ASN F 625 " NAG-THR " NAG C 603 " - " THR C 415 " Time building additional restraints: 11.84 Conformation dependent library (CDL) restraints added in 3.9 seconds 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5164 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 44 sheets defined 19.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.585A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.526A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.215A pdb=" N ALA B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 651 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.619A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.515A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 540 removed outlier: 3.752A pdb=" N THR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 651 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.548A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.111A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.673A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.624A pdb=" N ASN F 625 " --> pdb=" O MET F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.904A pdb=" N HIS G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.730A pdb=" N HIS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.562A pdb=" N ASP M 86 " --> pdb=" O THR M 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 30 Processing helix chain 'O' and resid 78 through 82 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.560A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 3.531A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.908A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.805A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 298 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 333 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.463A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.728A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB5, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.095A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 7.520A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 74 through 76 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AC3, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.926A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 298 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 329 through 333 current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'D' and resid 302 through 307 removed outlier: 6.618A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.822A pdb=" N TRP G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.907A pdb=" N MET G 100D" --> pdb=" O ILE G 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 12 current: chain 'I' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 47 current: chain 'I' and resid 97 through 99 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.756A pdb=" N ALA H 16 " --> pdb=" O LEU H 82C" (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 18 " --> pdb=" O ARG H 82A" (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG H 82A" --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL H 20 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N CYS H 22 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA H 24 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR H 77 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.055A pdb=" N PHE H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95 through 97 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AD6, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.801A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 9 through 12 current: chain 'O' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 44 through 47 current: chain 'O' and resid 97 through 99 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.748A pdb=" N ALA J 16 " --> pdb=" O LEU J 82C" (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 18 " --> pdb=" O ARG J 82A" (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG J 82A" --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL J 20 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP J 81 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N CYS J 22 " --> pdb=" O TYR J 79 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA J 24 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR J 77 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.293A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU J 45 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 12 current: chain 'N' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 48 current: chain 'N' and resid 95 through 97 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'N' and resid 18 through 21 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 removed outlier: 5.537A pdb=" N ALA K 16 " --> pdb=" O ASN K 82B" (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.231A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU K 45 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 9 through 12 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 95 through 97 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'P' and resid 18 through 22 672 hydrogen bonds defined for protein. 1704 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: 7.55 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4857 1.32 - 1.46: 8072 1.46 - 1.60: 11295 1.60 - 1.73: 97 1.73 - 1.87: 172 Bond restraints: 24493 Sorted by residual: bond pdb=" CB TYR O 48 " pdb=" CG TYR O 48 " ideal model delta sigma weight residual 1.512 1.340 0.172 2.20e-02 2.07e+03 6.13e+01 bond pdb=" NE1 TRP M 103 " pdb=" CE2 TRP M 103 " ideal model delta sigma weight residual 1.370 1.293 0.077 1.10e-02 8.26e+03 4.92e+01 bond pdb=" NE ARG A 66 " pdb=" CZ ARG A 66 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" NE ARG D 66 " pdb=" CZ ARG D 66 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.35e+01 bond pdb=" CB HIS H 35 " pdb=" CG HIS H 35 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.19e+01 ... (remaining 24488 not shown) Histogram of bond angle deviations from ideal: 75.90 - 93.33: 2 93.33 - 110.76: 9326 110.76 - 128.18: 23670 128.18 - 145.61: 281 145.61 - 163.04: 2 Bond angle restraints: 33281 Sorted by residual: angle pdb=" C8 NAG V 2 " pdb=" C7 NAG V 2 " pdb=" N2 NAG V 2 " ideal model delta sigma weight residual 115.06 163.04 -47.98 3.00e+00 1.11e-01 2.56e+02 angle pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " pdb=" O7 NAG V 2 " ideal model delta sigma weight residual 123.46 75.90 47.56 3.00e+00 1.11e-01 2.51e+02 angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 124.56 160.79 -36.23 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C8 NAG V 2 " pdb=" C7 NAG V 2 " pdb=" O7 NAG V 2 " ideal model delta sigma weight residual 121.48 87.14 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N LEU N 32 " pdb=" CA LEU N 32 " pdb=" C LEU N 32 " ideal model delta sigma weight residual 108.13 122.66 -14.53 1.72e+00 3.38e-01 7.14e+01 ... (remaining 33276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 15571 21.47 - 42.93: 503 42.93 - 64.40: 115 64.40 - 85.87: 234 85.87 - 107.33: 152 Dihedral angle restraints: 16575 sinusoidal: 8537 harmonic: 8038 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 146.42 -53.42 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 144.01 -51.01 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA ASN D 396 " pdb=" C ASN D 396 " pdb=" N ASP D 397 " pdb=" CA ASP D 397 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 16572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2794 0.122 - 0.244: 799 0.244 - 0.365: 387 0.365 - 0.487: 171 0.487 - 0.609: 21 Chirality restraints: 4172 Sorted by residual: chirality pdb=" C1 NAG 8 2 " pdb=" O4 NAG 8 1 " pdb=" C2 NAG 8 2 " pdb=" O5 NAG 8 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.14e+02 chirality pdb=" C1 NAG 0 2 " pdb=" O4 NAG 0 1 " pdb=" C2 NAG 0 2 " pdb=" O5 NAG 0 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.18e+02 ... (remaining 4169 not shown) Planarity restraints: 4061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 8 1 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG 8 1 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG 8 1 " -0.092 2.00e-02 2.50e+03 pdb=" N2 NAG 8 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG 8 1 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 8 2 " -0.327 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG 8 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG 8 2 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG 8 2 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG 8 2 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 606 " -0.188 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C7 NAG D 606 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 606 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG D 606 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG D 606 " 0.023 2.00e-02 2.50e+03 ... (remaining 4058 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 92 2.57 - 3.15: 20019 3.15 - 3.73: 36228 3.73 - 4.32: 55952 4.32 - 4.90: 84180 Nonbonded interactions: 196471 Sorted by model distance: nonbonded pdb=" OD1 ASP K 101 " pdb=" CG2 VAL P 46 " model vdw 1.982 3.460 nonbonded pdb=" NE1 TRP K 100H" pdb=" OD2 ASP K 101 " model vdw 2.123 2.520 nonbonded pdb=" OD2 ASP M 72 " pdb=" NZ LYS M 75 " model vdw 2.383 2.520 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.395 2.520 nonbonded pdb=" N TYR N 30 " pdb=" N ASP N 31 " model vdw 2.400 2.560 ... (remaining 196466 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 '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain '9' selection = chain 'AA' selection = chain 'Q' selection = chain 'W' selection = chain 'g' selection = chain 'l' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = (chain 'A' and (resid 35 through 502 or resid 601 through 603)) selection = chain 'C' selection = (chain 'D' and (resid 35 through 502 or resid 601 through 603)) } ncs_group { reference = (chain 'B' and (resid 523 through 653 or resid 702 through 703)) selection = chain 'E' selection = (chain 'F' and (resid 523 through 653 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.650 Check model and map are aligned: 0.360 Set scattering table: 0.240 Process input model: 63.390 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.570 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.024 0.174 24493 Z= 1.555 Angle : 1.917 47.982 33281 Z= 1.198 Chirality : 0.160 0.609 4172 Planarity : 0.011 0.303 3994 Dihedral : 19.121 107.331 11291 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.41 % Allowed : 0.94 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2731 helix: 0.29 (0.24), residues: 378 sheet: 0.40 (0.16), residues: 948 loop : 0.10 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.010 TRP A 479 HIS 0.018 0.003 HIS J 35 PHE 0.056 0.007 PHE G 78 TYR 0.083 0.010 TYR L 30 ARG 0.015 0.001 ARG G 100F *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 720 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9463 (mt) cc_final: 0.9245 (mm) REVERT: A 217 TYR cc_start: 0.7609 (m-80) cc_final: 0.6984 (m-10) REVERT: A 251 ILE cc_start: 0.9505 (mt) cc_final: 0.9300 (pt) REVERT: A 315 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7798 (mtp85) REVERT: C 69 TRP cc_start: 0.8516 (m-90) cc_final: 0.7925 (m-90) REVERT: C 86 LEU cc_start: 0.9584 (mt) cc_final: 0.9332 (mp) REVERT: C 373 MET cc_start: 0.8411 (mtm) cc_final: 0.8105 (mtp) REVERT: C 491 ILE cc_start: 0.9350 (mt) cc_final: 0.9102 (mm) REVERT: E 586 TYR cc_start: 0.9244 (t80) cc_final: 0.8739 (t80) REVERT: E 591 GLN cc_start: 0.8852 (tt0) cc_final: 0.8593 (tm-30) REVERT: E 595 ILE cc_start: 0.8913 (mt) cc_final: 0.8625 (mm) REVERT: E 601 LYS cc_start: 0.8861 (mttt) cc_final: 0.8549 (mmmt) REVERT: D 69 TRP cc_start: 0.7613 (m-90) cc_final: 0.7213 (m-90) REVERT: D 373 MET cc_start: 0.8178 (mmm) cc_final: 0.7944 (mmt) REVERT: D 381 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7242 (mt-10) REVERT: D 460 SER cc_start: 0.7710 (m) cc_final: 0.7329 (p) REVERT: F 530 MET cc_start: 0.9282 (mtm) cc_final: 0.8894 (mtm) REVERT: F 625 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7686 (t160) REVERT: F 630 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8498 (mt-10) REVERT: F 648 GLU cc_start: 0.8838 (mm-30) cc_final: 0.7848 (mm-30) REVERT: G 4 LEU cc_start: 0.8243 (mt) cc_final: 0.7961 (mp) REVERT: G 29 ILE cc_start: 0.9086 (pt) cc_final: 0.8106 (pt) REVERT: G 50 TYR cc_start: 0.7740 (p90) cc_final: 0.7221 (p90) REVERT: G 53 PHE cc_start: 0.7690 (t80) cc_final: 0.7059 (t80) REVERT: G 58 ASN cc_start: 0.7311 (t0) cc_final: 0.6714 (m-40) REVERT: G 59 TYR cc_start: 0.7633 (m-80) cc_final: 0.6981 (m-80) REVERT: I 25 ASN cc_start: 0.8950 (t0) cc_final: 0.8330 (m-40) REVERT: I 60 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: I 81 ASP cc_start: 0.8759 (m-30) cc_final: 0.8377 (m-30) REVERT: I 82 GLU cc_start: 0.8576 (tt0) cc_final: 0.8239 (tp30) REVERT: I 86 TYR cc_start: 0.8143 (m-80) cc_final: 0.7752 (m-80) REVERT: I 91 ASP cc_start: 0.7553 (t0) cc_final: 0.6504 (p0) REVERT: I 95 ASP cc_start: 0.8157 (t0) cc_final: 0.7119 (t70) REVERT: I 105 VAL cc_start: 0.8276 (t) cc_final: 0.7363 (p) REVERT: H 29 PHE cc_start: 0.8783 (t80) cc_final: 0.8033 (t80) REVERT: H 48 ILE cc_start: 0.9261 (mt) cc_final: 0.8965 (mp) REVERT: H 71 ARG cc_start: 0.8419 (ppt90) cc_final: 0.7987 (ptt90) REVERT: H 86 ASP cc_start: 0.8788 (m-30) cc_final: 0.8274 (m-30) REVERT: H 112 SER cc_start: 0.7932 (t) cc_final: 0.7415 (m) REVERT: L 36 TYR cc_start: 0.8645 (m-80) cc_final: 0.8435 (m-80) REVERT: L 62 PHE cc_start: 0.8540 (m-80) cc_final: 0.7948 (m-10) REVERT: L 80 VAL cc_start: 0.7954 (t) cc_final: 0.6675 (p) REVERT: L 89 TYR cc_start: 0.8762 (t80) cc_final: 0.8226 (t80) REVERT: M 11 LEU cc_start: 0.6984 (tp) cc_final: 0.6773 (mt) REVERT: M 29 ILE cc_start: 0.8842 (pt) cc_final: 0.8328 (pt) REVERT: M 53 PHE cc_start: 0.8070 (t80) cc_final: 0.7717 (t80) REVERT: M 64 LYS cc_start: 0.8325 (tttt) cc_final: 0.7972 (tptt) REVERT: M 100 ARG cc_start: 0.6698 (mtp85) cc_final: 0.6373 (mtt180) REVERT: M 107 THR cc_start: 0.9265 (t) cc_final: 0.9035 (p) REVERT: O 34 TRP cc_start: 0.8818 (m100) cc_final: 0.8549 (m100) REVERT: O 95 ASP cc_start: 0.8274 (t0) cc_final: 0.7383 (t0) REVERT: J 12 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8497 (mmtm) REVERT: J 27 TYR cc_start: 0.4984 (t80) cc_final: 0.4436 (t80) REVERT: J 29 PHE cc_start: 0.7757 (t80) cc_final: 0.7227 (t80) REVERT: J 31 LYS cc_start: 0.8820 (mttt) cc_final: 0.8476 (mtmt) REVERT: J 71 ARG cc_start: 0.8407 (ppt90) cc_final: 0.7861 (ptt90) REVERT: J 80 MET cc_start: 0.8688 (ttp) cc_final: 0.8339 (ttp) REVERT: J 86 ASP cc_start: 0.9148 (m-30) cc_final: 0.8348 (m-30) REVERT: N 18 ILE cc_start: 0.8664 (pt) cc_final: 0.8386 (mp) REVERT: N 36 TYR cc_start: 0.8597 (m-80) cc_final: 0.8029 (m-80) REVERT: N 61 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: N 86 TYR cc_start: 0.7856 (m-80) cc_final: 0.7568 (m-10) REVERT: N 103 LEU cc_start: 0.8690 (tp) cc_final: 0.8400 (tt) REVERT: K 3 GLN cc_start: 0.8393 (tt0) cc_final: 0.7863 (tm-30) REVERT: K 5 LEU cc_start: 0.9298 (tp) cc_final: 0.9050 (tp) REVERT: K 6 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6501 (mt-10) REVERT: K 25 SER cc_start: 0.8384 (m) cc_final: 0.6895 (p) REVERT: K 51 ILE cc_start: 0.9051 (tt) cc_final: 0.8829 (tp) REVERT: K 72 ASP cc_start: 0.8199 (t0) cc_final: 0.7782 (t0) REVERT: K 89 VAL cc_start: 0.8631 (t) cc_final: 0.8375 (p) REVERT: P 80 VAL cc_start: 0.8656 (t) cc_final: 0.8431 (p) REVERT: P 89 TYR cc_start: 0.9080 (t80) cc_final: 0.8879 (t80) outliers start: 10 outliers final: 2 residues processed: 729 average time/residue: 0.4289 time to fit residues: 462.9349 Evaluate side-chains 354 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 350 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 425 ASN B 543 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 ASN G 100CASN I 6 GLN I 36 GLN I 88 GLN L 37 GLN L 60 HIS O 36 GLN O 68 ASN N 37 GLN P 37 GLN P 79 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24493 Z= 0.273 Angle : 0.959 44.440 33281 Z= 0.445 Chirality : 0.057 0.448 4172 Planarity : 0.005 0.068 3994 Dihedral : 16.197 84.041 6207 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.83 % Allowed : 10.50 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2731 helix: 0.78 (0.25), residues: 403 sheet: 0.54 (0.17), residues: 893 loop : -0.32 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 100H HIS 0.011 0.001 HIS C 330 PHE 0.025 0.002 PHE G 78 TYR 0.041 0.002 TYR L 30 ARG 0.015 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 428 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8145 (t0) REVERT: A 376 PHE cc_start: 0.7947 (t80) cc_final: 0.7497 (t80) REVERT: B 585 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8269 (mtp85) REVERT: B 651 ASN cc_start: 0.7268 (m-40) cc_final: 0.6983 (m-40) REVERT: C 69 TRP cc_start: 0.8388 (m-90) cc_final: 0.7998 (m-90) REVERT: C 98 ASN cc_start: 0.8676 (t0) cc_final: 0.8238 (t0) REVERT: C 114 GLN cc_start: 0.8867 (tp40) cc_final: 0.8560 (tm-30) REVERT: C 449 ILE cc_start: 0.9360 (mt) cc_final: 0.9117 (tt) REVERT: E 577 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8142 (tm-30) REVERT: E 590 GLN cc_start: 0.8835 (tp40) cc_final: 0.8603 (tm-30) REVERT: E 601 LYS cc_start: 0.8975 (mttt) cc_final: 0.8557 (mmmm) REVERT: D 373 MET cc_start: 0.7969 (mmm) cc_final: 0.7610 (mpp) REVERT: D 381 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7208 (mt-10) REVERT: F 530 MET cc_start: 0.9243 (mtm) cc_final: 0.8664 (mtm) REVERT: F 577 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8583 (tm-30) REVERT: F 584 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8378 (mt-10) REVERT: F 635 ILE cc_start: 0.9447 (pt) cc_final: 0.9219 (pt) REVERT: F 648 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 53 PHE cc_start: 0.7362 (t80) cc_final: 0.6846 (t80) REVERT: G 59 TYR cc_start: 0.7651 (m-80) cc_final: 0.7058 (m-80) REVERT: I 16 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8514 (ptmt) REVERT: I 25 ASN cc_start: 0.8723 (t0) cc_final: 0.8318 (m-40) REVERT: I 82 GLU cc_start: 0.8662 (tt0) cc_final: 0.8258 (tp30) REVERT: I 88 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: I 105 VAL cc_start: 0.8337 (t) cc_final: 0.7200 (p) REVERT: H 10 GLU cc_start: 0.7665 (tp30) cc_final: 0.7315 (tp30) REVERT: H 29 PHE cc_start: 0.8536 (t80) cc_final: 0.7974 (t80) REVERT: H 30 THR cc_start: 0.9439 (p) cc_final: 0.9186 (t) REVERT: H 112 SER cc_start: 0.8052 (t) cc_final: 0.7614 (m) REVERT: L 2 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5441 (t80) REVERT: L 36 TYR cc_start: 0.8454 (m-80) cc_final: 0.8211 (m-80) REVERT: L 80 VAL cc_start: 0.7403 (t) cc_final: 0.7032 (p) REVERT: L 89 TYR cc_start: 0.8446 (t80) cc_final: 0.8174 (t80) REVERT: M 29 ILE cc_start: 0.8553 (pt) cc_final: 0.8265 (pt) REVERT: M 43 LYS cc_start: 0.8543 (mtpp) cc_final: 0.7818 (ptpp) REVERT: M 53 PHE cc_start: 0.7940 (t80) cc_final: 0.7020 (t80) REVERT: M 64 LYS cc_start: 0.8284 (tttt) cc_final: 0.8054 (tptt) REVERT: O 68 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7720 (m-40) REVERT: O 72 LEU cc_start: 0.9519 (tp) cc_final: 0.8882 (tp) REVERT: O 76 ARG cc_start: 0.7467 (mmp80) cc_final: 0.7161 (mmp80) REVERT: O 78 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7541 (mp0) REVERT: O 94 ARG cc_start: 0.8872 (mmp80) cc_final: 0.8440 (mmp80) REVERT: O 95 ASP cc_start: 0.8394 (t0) cc_final: 0.7486 (t0) REVERT: J 12 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8602 (mmtm) REVERT: J 30 THR cc_start: 0.9350 (p) cc_final: 0.9080 (t) REVERT: J 52 ASN cc_start: 0.8965 (t0) cc_final: 0.8240 (t0) REVERT: J 86 ASP cc_start: 0.8901 (m-30) cc_final: 0.8660 (m-30) REVERT: N 36 TYR cc_start: 0.8736 (m-80) cc_final: 0.8494 (m-80) REVERT: K 3 GLN cc_start: 0.8442 (tt0) cc_final: 0.8223 (tm-30) REVERT: K 72 ASP cc_start: 0.8171 (t0) cc_final: 0.7523 (t0) REVERT: K 100 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8087 (mp0) REVERT: P 79 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6380 (mp10) REVERT: P 91 TYR cc_start: 0.9020 (t80) cc_final: 0.8662 (t80) outliers start: 69 outliers final: 38 residues processed: 476 average time/residue: 0.3505 time to fit residues: 257.0541 Evaluate side-chains 372 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 329 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 60 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 243 optimal weight: 0.0040 chunk 83 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN C 330 HIS ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 413 HIS G 100CASN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS N 37 GLN P 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24493 Z= 0.350 Angle : 0.931 43.783 33281 Z= 0.424 Chirality : 0.055 0.415 4172 Planarity : 0.005 0.064 3994 Dihedral : 11.739 71.102 6202 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 3.41 % Allowed : 12.72 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2731 helix: 1.42 (0.27), residues: 369 sheet: 0.38 (0.17), residues: 903 loop : -0.56 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 69 HIS 0.011 0.002 HIS L 60 PHE 0.023 0.002 PHE G 78 TYR 0.029 0.002 TYR K 27 ARG 0.008 0.001 ARG I 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 349 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.8030 (t80) cc_final: 0.7728 (t80) REVERT: B 530 MET cc_start: 0.8779 (mmt) cc_final: 0.8458 (mmt) REVERT: B 585 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8382 (mtp85) REVERT: B 621 MET cc_start: 0.8510 (tpt) cc_final: 0.8304 (tpt) REVERT: B 626 MET cc_start: 0.8194 (mtp) cc_final: 0.7822 (ttm) REVERT: C 69 TRP cc_start: 0.8370 (m-90) cc_final: 0.7990 (m-90) REVERT: C 98 ASN cc_start: 0.8737 (t0) cc_final: 0.8314 (t0) REVERT: C 114 GLN cc_start: 0.8903 (tp40) cc_final: 0.8588 (tm-30) REVERT: E 577 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8192 (tm-30) REVERT: E 601 LYS cc_start: 0.9043 (mttt) cc_final: 0.8819 (mmtp) REVERT: D 269 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: F 530 MET cc_start: 0.9296 (mtm) cc_final: 0.8745 (mtm) REVERT: F 570 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8133 (t) REVERT: F 574 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8768 (UNCLASSIFIED) REVERT: F 577 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8595 (tm-30) REVERT: F 584 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8227 (mt-10) REVERT: F 588 ARG cc_start: 0.9172 (ttt-90) cc_final: 0.8914 (ttt90) REVERT: F 635 ILE cc_start: 0.9549 (pt) cc_final: 0.9330 (pt) REVERT: F 648 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8359 (mm-30) REVERT: G 78 PHE cc_start: 0.7187 (m-80) cc_final: 0.3900 (m-80) REVERT: G 100 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6653 (mmm) REVERT: G 105 GLN cc_start: 0.8814 (pt0) cc_final: 0.8544 (pp30) REVERT: I 25 ASN cc_start: 0.8762 (t0) cc_final: 0.8458 (m-40) REVERT: I 60 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: H 13 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8814 (mmmt) REVERT: H 30 THR cc_start: 0.9538 (p) cc_final: 0.9262 (t) REVERT: H 112 SER cc_start: 0.7981 (t) cc_final: 0.7761 (m) REVERT: L 2 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5662 (t80) REVERT: L 89 TYR cc_start: 0.8600 (t80) cc_final: 0.8393 (t80) REVERT: M 29 ILE cc_start: 0.8773 (pt) cc_final: 0.8516 (pt) REVERT: M 64 LYS cc_start: 0.8520 (tttt) cc_final: 0.8259 (tptt) REVERT: M 100 MET cc_start: 0.7286 (mtt) cc_final: 0.6941 (ttm) REVERT: O 72 LEU cc_start: 0.9425 (tp) cc_final: 0.9165 (tp) REVERT: O 76 ARG cc_start: 0.7610 (mmp80) cc_final: 0.7288 (mmp80) REVERT: O 94 ARG cc_start: 0.9045 (mmp80) cc_final: 0.8754 (mmp80) REVERT: O 95 ASP cc_start: 0.8646 (t0) cc_final: 0.7741 (t70) REVERT: J 12 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8603 (mmtm) REVERT: J 27 TYR cc_start: 0.4616 (t80) cc_final: 0.4409 (t80) REVERT: J 30 THR cc_start: 0.9484 (p) cc_final: 0.9133 (t) REVERT: J 52 ASN cc_start: 0.8976 (t0) cc_final: 0.8239 (t0) REVERT: J 76 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8717 (mt-10) REVERT: J 80 MET cc_start: 0.8248 (ttp) cc_final: 0.7875 (ptm) REVERT: J 86 ASP cc_start: 0.9034 (m-30) cc_final: 0.8747 (m-30) REVERT: N 93 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7841 (t70) REVERT: N 94 MET cc_start: 0.8689 (ttt) cc_final: 0.8477 (ttp) REVERT: K 3 GLN cc_start: 0.8519 (tt0) cc_final: 0.8239 (tm-30) REVERT: K 72 ASP cc_start: 0.8028 (t0) cc_final: 0.7286 (t0) outliers start: 83 outliers final: 55 residues processed: 406 average time/residue: 0.3532 time to fit residues: 222.4427 Evaluate side-chains 366 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 306 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 590 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 302 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 352 GLN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN J 39 GLN J 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 24493 Z= 0.443 Angle : 0.952 43.873 33281 Z= 0.437 Chirality : 0.055 0.436 4172 Planarity : 0.006 0.099 3994 Dihedral : 9.261 59.806 6200 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 4.19 % Allowed : 14.07 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2731 helix: 1.38 (0.27), residues: 375 sheet: 0.19 (0.17), residues: 892 loop : -0.92 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O 34 HIS 0.012 0.002 HIS O 33 PHE 0.027 0.003 PHE G 78 TYR 0.036 0.003 TYR J 27 ARG 0.008 0.001 ARG J 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 321 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.8068 (t80) cc_final: 0.7789 (t80) REVERT: B 530 MET cc_start: 0.8898 (mmm) cc_final: 0.8652 (mmt) REVERT: B 585 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8382 (mtp85) REVERT: C 69 TRP cc_start: 0.8326 (m-90) cc_final: 0.7754 (m-90) REVERT: C 98 ASN cc_start: 0.8771 (t0) cc_final: 0.8519 (t0) REVERT: C 114 GLN cc_start: 0.8959 (tp40) cc_final: 0.8753 (tm-30) REVERT: E 577 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8302 (tm-30) REVERT: E 601 LYS cc_start: 0.9070 (mttt) cc_final: 0.8752 (mmmm) REVERT: D 269 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: F 530 MET cc_start: 0.9302 (mtm) cc_final: 0.8836 (mtm) REVERT: F 574 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8757 (mtmt) REVERT: F 577 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 584 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8217 (mt-10) REVERT: F 588 ARG cc_start: 0.9215 (ttt-90) cc_final: 0.8997 (ttt90) REVERT: F 621 MET cc_start: 0.9115 (tpt) cc_final: 0.8679 (tpp) REVERT: F 648 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8522 (mm-30) REVERT: G 78 PHE cc_start: 0.6855 (m-80) cc_final: 0.5985 (m-80) REVERT: G 100 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6869 (mmm) REVERT: I 25 ASN cc_start: 0.8745 (t0) cc_final: 0.8496 (m-40) REVERT: H 13 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8819 (mmmt) REVERT: H 30 THR cc_start: 0.9661 (p) cc_final: 0.9403 (t) REVERT: H 97 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7505 (mtp180) REVERT: H 112 SER cc_start: 0.8051 (t) cc_final: 0.7794 (m) REVERT: L 2 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.5609 (t80) REVERT: L 49 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7534 (t80) REVERT: M 29 ILE cc_start: 0.8923 (pt) cc_final: 0.8720 (pt) REVERT: M 64 LYS cc_start: 0.8766 (tttt) cc_final: 0.8550 (tppt) REVERT: O 94 ARG cc_start: 0.9067 (mmp80) cc_final: 0.8816 (mmp80) REVERT: J 12 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8547 (mmtm) REVERT: J 31 LYS cc_start: 0.9150 (tppp) cc_final: 0.8286 (tptt) REVERT: J 52 ASN cc_start: 0.9037 (t0) cc_final: 0.8358 (t0) REVERT: J 86 ASP cc_start: 0.8930 (m-30) cc_final: 0.8612 (m-30) REVERT: J 94 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7307 (mmm-85) REVERT: N 94 MET cc_start: 0.8746 (ttt) cc_final: 0.8495 (ttp) REVERT: K 3 GLN cc_start: 0.8405 (tt0) cc_final: 0.8171 (tm-30) REVERT: K 25 SER cc_start: 0.8860 (t) cc_final: 0.8649 (t) REVERT: K 72 ASP cc_start: 0.8128 (t0) cc_final: 0.7565 (t0) REVERT: K 100 TRP cc_start: 0.8297 (t60) cc_final: 0.8023 (t60) REVERT: P 49 PHE cc_start: 0.8368 (t80) cc_final: 0.7772 (t80) outliers start: 102 outliers final: 68 residues processed: 394 average time/residue: 0.3496 time to fit residues: 216.0465 Evaluate side-chains 350 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 277 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain P residue 51 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 352 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 GLN L 37 GLN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 24493 Z= 0.438 Angle : 0.931 43.786 33281 Z= 0.430 Chirality : 0.053 0.406 4172 Planarity : 0.005 0.046 3994 Dihedral : 8.689 59.545 6200 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 3.98 % Allowed : 15.43 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2731 helix: 1.28 (0.27), residues: 376 sheet: 0.04 (0.17), residues: 854 loop : -1.13 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP O 34 HIS 0.010 0.002 HIS O 33 PHE 0.017 0.002 PHE A 93 TYR 0.050 0.003 TYR J 27 ARG 0.007 0.001 ARG I 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 299 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.8219 (t80) cc_final: 0.8015 (t80) REVERT: A 475 MET cc_start: 0.8922 (mmm) cc_final: 0.8387 (mmt) REVERT: B 530 MET cc_start: 0.8924 (mmm) cc_final: 0.8649 (mmt) REVERT: B 585 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8444 (mtp85) REVERT: C 69 TRP cc_start: 0.8241 (m-90) cc_final: 0.7536 (m-90) REVERT: C 363 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: E 536 THR cc_start: 0.8519 (m) cc_final: 0.8221 (p) REVERT: E 577 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8312 (tm-30) REVERT: E 601 LYS cc_start: 0.9232 (mttt) cc_final: 0.8881 (mmmm) REVERT: F 530 MET cc_start: 0.9228 (mtm) cc_final: 0.8762 (mtm) REVERT: F 535 MET cc_start: 0.8956 (mmp) cc_final: 0.8699 (mmm) REVERT: F 574 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8702 (mtmt) REVERT: F 577 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8554 (tm-30) REVERT: F 584 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8242 (mt-10) REVERT: F 588 ARG cc_start: 0.9207 (ttt-90) cc_final: 0.8973 (ttt90) REVERT: F 621 MET cc_start: 0.9286 (tpt) cc_final: 0.8900 (tpt) REVERT: G 100 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6738 (mmm) REVERT: I 82 GLU cc_start: 0.8922 (tt0) cc_final: 0.8455 (tp30) REVERT: H 13 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8850 (mmmt) REVERT: H 23 GLU cc_start: 0.7779 (mp0) cc_final: 0.7472 (mp0) REVERT: H 112 SER cc_start: 0.7944 (t) cc_final: 0.7729 (m) REVERT: L 2 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5630 (t80) REVERT: L 49 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7564 (t80) REVERT: M 13 LYS cc_start: 0.9261 (tppt) cc_final: 0.9051 (tppt) REVERT: M 64 LYS cc_start: 0.8785 (tttt) cc_final: 0.8547 (tptt) REVERT: M 77 GLN cc_start: 0.9041 (mm110) cc_final: 0.8605 (mm-40) REVERT: M 100 MET cc_start: 0.7478 (mtt) cc_final: 0.7142 (ttm) REVERT: O 60 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8101 (mtm-85) REVERT: O 94 ARG cc_start: 0.9063 (mmp80) cc_final: 0.8823 (mmp80) REVERT: J 12 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8667 (mptt) REVERT: J 31 LYS cc_start: 0.9226 (tppp) cc_final: 0.8480 (tptt) REVERT: J 32 TYR cc_start: 0.4531 (p90) cc_final: 0.4221 (p90) REVERT: J 86 ASP cc_start: 0.8781 (m-30) cc_final: 0.8513 (m-30) REVERT: J 94 ARG cc_start: 0.7905 (tpp80) cc_final: 0.7518 (mmm-85) REVERT: N 94 MET cc_start: 0.8765 (ttt) cc_final: 0.8512 (ttp) REVERT: K 3 GLN cc_start: 0.8528 (tt0) cc_final: 0.8222 (tm-30) REVERT: K 25 SER cc_start: 0.9052 (t) cc_final: 0.8842 (t) REVERT: K 72 ASP cc_start: 0.8279 (t0) cc_final: 0.7718 (t0) REVERT: K 100 TRP cc_start: 0.8349 (t60) cc_final: 0.8125 (t60) REVERT: P 49 PHE cc_start: 0.8350 (t80) cc_final: 0.7754 (t80) outliers start: 97 outliers final: 73 residues processed: 370 average time/residue: 0.3383 time to fit residues: 197.7157 Evaluate side-chains 352 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 275 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain P residue 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS C 67 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 GLN O 26 ASN O 36 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24493 Z= 0.243 Angle : 0.832 43.797 33281 Z= 0.376 Chirality : 0.051 0.376 4172 Planarity : 0.005 0.122 3994 Dihedral : 7.888 58.483 6200 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 3.16 % Allowed : 16.54 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2731 helix: 1.64 (0.28), residues: 369 sheet: 0.10 (0.17), residues: 884 loop : -1.03 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 34 HIS 0.005 0.001 HIS J 35 PHE 0.040 0.002 PHE G 78 TYR 0.041 0.002 TYR J 27 ARG 0.010 0.001 ARG J 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 315 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8741 (t0) cc_final: 0.8388 (t0) REVERT: A 381 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: A 475 MET cc_start: 0.8870 (mmm) cc_final: 0.8221 (mmt) REVERT: B 530 MET cc_start: 0.8826 (mmm) cc_final: 0.8568 (mmt) REVERT: B 585 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8411 (mtp85) REVERT: B 595 ILE cc_start: 0.9176 (tp) cc_final: 0.8854 (tp) REVERT: C 69 TRP cc_start: 0.8172 (m-90) cc_final: 0.7570 (m-90) REVERT: C 363 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: E 577 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 601 LYS cc_start: 0.9225 (mttt) cc_final: 0.8835 (mmmm) REVERT: D 47 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7846 (tm-30) REVERT: F 530 MET cc_start: 0.9179 (mtm) cc_final: 0.8615 (mtm) REVERT: F 574 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8699 (mtmt) REVERT: F 577 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 584 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8262 (mt-10) REVERT: F 588 ARG cc_start: 0.9159 (ttt-90) cc_final: 0.8928 (ttt90) REVERT: F 621 MET cc_start: 0.9273 (tpt) cc_final: 0.8897 (tpt) REVERT: F 648 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8369 (mm-30) REVERT: F 651 ASN cc_start: 0.7934 (m110) cc_final: 0.7604 (t0) REVERT: G 100 ASP cc_start: 0.7949 (m-30) cc_final: 0.7695 (t0) REVERT: G 100 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6931 (mmm) REVERT: G 103 TRP cc_start: 0.7186 (t-100) cc_final: 0.6896 (t-100) REVERT: G 105 GLN cc_start: 0.9054 (pt0) cc_final: 0.8664 (pp30) REVERT: I 38 LYS cc_start: 0.6929 (tmtt) cc_final: 0.6564 (tmtt) REVERT: I 82 GLU cc_start: 0.8919 (tt0) cc_final: 0.8402 (tp30) REVERT: H 13 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8848 (mmmt) REVERT: L 2 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.5552 (t80) REVERT: L 49 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7519 (t80) REVERT: M 64 LYS cc_start: 0.8700 (tttt) cc_final: 0.8475 (tppt) REVERT: M 100 MET cc_start: 0.7284 (mtt) cc_final: 0.7080 (ttm) REVERT: O 60 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.8092 (mtm-85) REVERT: O 94 ARG cc_start: 0.9017 (mmp80) cc_final: 0.8809 (mmp80) REVERT: J 3 GLN cc_start: 0.7777 (mp10) cc_final: 0.7569 (mm-40) REVERT: J 12 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8561 (mptt) REVERT: J 31 LYS cc_start: 0.9255 (tppp) cc_final: 0.8488 (tptt) REVERT: J 52 ASN cc_start: 0.8911 (t0) cc_final: 0.8250 (t0) REVERT: J 86 ASP cc_start: 0.8766 (m-30) cc_final: 0.8523 (m-30) REVERT: J 100 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8558 (mm-30) REVERT: N 88 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7409 (m) REVERT: N 94 MET cc_start: 0.8778 (ttt) cc_final: 0.8519 (ttp) REVERT: K 3 GLN cc_start: 0.8610 (tt0) cc_final: 0.8261 (tm-30) REVERT: K 72 ASP cc_start: 0.8161 (t0) cc_final: 0.7578 (t0) REVERT: K 100 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8136 (mp0) REVERT: P 49 PHE cc_start: 0.8053 (t80) cc_final: 0.7710 (t80) outliers start: 77 outliers final: 53 residues processed: 369 average time/residue: 0.3513 time to fit residues: 203.3896 Evaluate side-chains 343 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 284 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 260 optimal weight: 0.0060 chunk 162 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 170 GLN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24493 Z= 0.192 Angle : 0.815 43.650 33281 Z= 0.367 Chirality : 0.050 0.376 4172 Planarity : 0.004 0.064 3994 Dihedral : 7.370 59.719 6200 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 2.30 % Allowed : 17.40 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2731 helix: 1.59 (0.28), residues: 377 sheet: 0.15 (0.17), residues: 854 loop : -0.95 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 69 HIS 0.005 0.001 HIS J 35 PHE 0.032 0.002 PHE G 78 TYR 0.051 0.002 TYR L 30 ARG 0.008 0.001 ARG J 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 324 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8666 (t0) cc_final: 0.8304 (t0) REVERT: B 530 MET cc_start: 0.8870 (mmm) cc_final: 0.8573 (mmt) REVERT: B 633 ARG cc_start: 0.8941 (mtp-110) cc_final: 0.8503 (mtm110) REVERT: C 69 TRP cc_start: 0.8053 (m-90) cc_final: 0.7641 (m-90) REVERT: C 363 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: E 577 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8089 (tm-30) REVERT: E 601 LYS cc_start: 0.9144 (mttt) cc_final: 0.8764 (mmmm) REVERT: F 530 MET cc_start: 0.9174 (mtm) cc_final: 0.8944 (mtm) REVERT: F 574 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8686 (mtmt) REVERT: F 584 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8375 (mt-10) REVERT: F 621 MET cc_start: 0.9266 (tpt) cc_final: 0.8873 (tpt) REVERT: G 78 PHE cc_start: 0.6319 (m-80) cc_final: 0.5663 (m-10) REVERT: G 100 ASP cc_start: 0.7951 (m-30) cc_final: 0.7720 (t0) REVERT: G 100 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6877 (mmm) REVERT: G 100 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.5983 (m-80) REVERT: G 105 GLN cc_start: 0.9072 (pt0) cc_final: 0.8646 (pp30) REVERT: H 13 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8773 (mmmt) REVERT: H 97 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7343 (mtp180) REVERT: L 2 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.5513 (t80) REVERT: L 49 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7533 (t80) REVERT: M 4 LEU cc_start: 0.8862 (mp) cc_final: 0.8451 (tt) REVERT: M 56 ASN cc_start: 0.8950 (m-40) cc_final: 0.8269 (t0) REVERT: M 64 LYS cc_start: 0.8628 (tttt) cc_final: 0.8426 (tppt) REVERT: M 77 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8475 (mm-40) REVERT: M 78 PHE cc_start: 0.7424 (m-10) cc_final: 0.7098 (m-10) REVERT: M 100 MET cc_start: 0.7171 (mtt) cc_final: 0.6917 (ttm) REVERT: O 60 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8151 (mtm-85) REVERT: O 94 ARG cc_start: 0.9060 (mmp80) cc_final: 0.8853 (mmp80) REVERT: J 3 GLN cc_start: 0.7747 (mp10) cc_final: 0.7456 (mp10) REVERT: J 12 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8483 (mptt) REVERT: J 31 LYS cc_start: 0.9254 (tppp) cc_final: 0.8828 (tmmt) REVERT: J 52 ASN cc_start: 0.8828 (t0) cc_final: 0.8171 (t0) REVERT: J 80 MET cc_start: 0.8709 (ttp) cc_final: 0.8462 (ttp) REVERT: J 86 ASP cc_start: 0.8753 (m-30) cc_final: 0.8484 (m-30) REVERT: J 100 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8609 (mm-30) REVERT: N 94 MET cc_start: 0.8781 (ttt) cc_final: 0.8543 (ttp) REVERT: K 3 GLN cc_start: 0.8566 (tt0) cc_final: 0.8256 (tm-30) REVERT: K 62 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.7935 (p0) REVERT: K 72 ASP cc_start: 0.8135 (t0) cc_final: 0.7580 (t0) outliers start: 56 outliers final: 44 residues processed: 366 average time/residue: 0.3528 time to fit residues: 202.2238 Evaluate side-chains 338 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 287 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 99 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 165 optimal weight: 9.9990 chunk 177 optimal weight: 30.0000 chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24493 Z= 0.294 Angle : 0.847 43.495 33281 Z= 0.384 Chirality : 0.051 0.372 4172 Planarity : 0.004 0.048 3994 Dihedral : 7.344 58.957 6200 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 3.36 % Allowed : 17.36 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2731 helix: 1.56 (0.28), residues: 375 sheet: 0.14 (0.18), residues: 858 loop : -0.96 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 69 HIS 0.007 0.001 HIS O 33 PHE 0.024 0.002 PHE G 100H TYR 0.020 0.002 TYR O 86 ARG 0.019 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 297 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8742 (t0) cc_final: 0.8389 (t0) REVERT: A 381 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: B 530 MET cc_start: 0.8781 (mmm) cc_final: 0.8532 (mmt) REVERT: C 69 TRP cc_start: 0.8178 (m-90) cc_final: 0.7662 (m-90) REVERT: C 363 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: E 577 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8113 (tm-30) REVERT: E 585 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8314 (mtp-110) REVERT: E 601 LYS cc_start: 0.9213 (mttt) cc_final: 0.8843 (mmmm) REVERT: F 530 MET cc_start: 0.9219 (mtm) cc_final: 0.8683 (mtm) REVERT: F 574 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8636 (mtmm) REVERT: F 584 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8199 (mt-10) REVERT: F 621 MET cc_start: 0.9250 (tpt) cc_final: 0.8836 (tpt) REVERT: G 100 ASP cc_start: 0.7834 (m-30) cc_final: 0.7546 (t0) REVERT: G 100 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6745 (mmm) REVERT: G 105 GLN cc_start: 0.9100 (pt0) cc_final: 0.8685 (pp30) REVERT: I 82 GLU cc_start: 0.8912 (tt0) cc_final: 0.8416 (tp30) REVERT: H 97 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: L 2 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5571 (t80) REVERT: L 49 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7488 (t80) REVERT: M 56 ASN cc_start: 0.9008 (m-40) cc_final: 0.8403 (t0) REVERT: M 64 LYS cc_start: 0.8681 (tttt) cc_final: 0.8466 (tppt) REVERT: O 60 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8147 (mtm-85) REVERT: O 94 ARG cc_start: 0.9102 (mmp80) cc_final: 0.8877 (mmp80) REVERT: J 3 GLN cc_start: 0.7731 (mp10) cc_final: 0.7397 (mp10) REVERT: J 12 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8501 (mptt) REVERT: J 31 LYS cc_start: 0.9232 (tppp) cc_final: 0.8796 (tmmt) REVERT: J 52 ASN cc_start: 0.8892 (t0) cc_final: 0.8265 (t0) REVERT: J 86 ASP cc_start: 0.8755 (m-30) cc_final: 0.8480 (m-30) REVERT: J 100 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8192 (mp0) REVERT: N 88 CYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7469 (m) REVERT: N 94 MET cc_start: 0.8801 (ttt) cc_final: 0.8567 (ttp) REVERT: K 3 GLN cc_start: 0.8513 (tt0) cc_final: 0.8237 (tm-30) REVERT: K 72 ASP cc_start: 0.8146 (t0) cc_final: 0.7594 (t0) REVERT: P 3 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8199 (mm-30) outliers start: 82 outliers final: 63 residues processed: 355 average time/residue: 0.3432 time to fit residues: 192.5042 Evaluate side-chains 353 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 283 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain K residue 99 TYR Chi-restraints excluded: chain P residue 95 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 8.9990 chunk 249 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24493 Z= 0.385 Angle : 0.899 43.483 33281 Z= 0.411 Chirality : 0.052 0.387 4172 Planarity : 0.004 0.051 3994 Dihedral : 7.670 59.890 6200 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.10 % Favored : 92.86 % Rotamer: Outliers : 3.24 % Allowed : 17.36 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2731 helix: 1.50 (0.28), residues: 364 sheet: -0.02 (0.17), residues: 890 loop : -1.13 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 100G HIS 0.005 0.001 HIS O 33 PHE 0.016 0.002 PHE M 78 TYR 0.071 0.002 TYR L 30 ARG 0.016 0.001 ARG B 633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 288 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8777 (t0) cc_final: 0.8379 (t0) REVERT: A 381 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 530 MET cc_start: 0.8772 (mmm) cc_final: 0.8505 (mmt) REVERT: C 69 TRP cc_start: 0.8310 (m-90) cc_final: 0.7680 (m-90) REVERT: C 363 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: E 575 GLN cc_start: 0.8861 (pp30) cc_final: 0.8518 (pp30) REVERT: E 577 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8233 (tm-30) REVERT: E 585 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8248 (mtp-110) REVERT: E 601 LYS cc_start: 0.9208 (mttt) cc_final: 0.8870 (mmmm) REVERT: F 530 MET cc_start: 0.9258 (mtm) cc_final: 0.8747 (mtm) REVERT: F 574 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8730 (mtmt) REVERT: F 584 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8238 (mt-10) REVERT: F 621 MET cc_start: 0.9270 (tpt) cc_final: 0.8820 (tpt) REVERT: G 100 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6687 (mmm) REVERT: I 82 GLU cc_start: 0.8910 (tt0) cc_final: 0.8426 (tp30) REVERT: L 2 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5661 (t80) REVERT: L 49 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7673 (t80) REVERT: M 56 ASN cc_start: 0.9078 (m-40) cc_final: 0.8501 (t0) REVERT: M 64 LYS cc_start: 0.8762 (tttt) cc_final: 0.8531 (tppt) REVERT: M 100 MET cc_start: 0.7357 (mtt) cc_final: 0.6784 (ttm) REVERT: O 94 ARG cc_start: 0.9094 (mmp80) cc_final: 0.8893 (mmp80) REVERT: J 3 GLN cc_start: 0.7696 (mp10) cc_final: 0.7356 (mp10) REVERT: J 6 GLU cc_start: 0.7946 (mp0) cc_final: 0.7545 (mp0) REVERT: J 12 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8516 (mptt) REVERT: J 31 LYS cc_start: 0.9191 (tppp) cc_final: 0.8915 (tmmt) REVERT: J 86 ASP cc_start: 0.8741 (m-30) cc_final: 0.8510 (m-30) REVERT: J 100 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8661 (mm-30) REVERT: N 94 MET cc_start: 0.8799 (ttt) cc_final: 0.8555 (ttp) REVERT: K 3 GLN cc_start: 0.8706 (tt0) cc_final: 0.8382 (tm-30) REVERT: K 72 ASP cc_start: 0.8258 (t0) cc_final: 0.7679 (t0) outliers start: 79 outliers final: 65 residues processed: 343 average time/residue: 0.3390 time to fit residues: 184.8631 Evaluate side-chains 344 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 274 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 99 TYR Chi-restraints excluded: chain P residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 247 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24493 Z= 0.196 Angle : 0.832 43.644 33281 Z= 0.376 Chirality : 0.050 0.355 4172 Planarity : 0.004 0.063 3994 Dihedral : 7.192 59.493 6200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.38 % Allowed : 18.34 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2731 helix: 1.95 (0.28), residues: 340 sheet: 0.01 (0.17), residues: 888 loop : -1.01 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 69 HIS 0.004 0.001 HIS O 33 PHE 0.022 0.001 PHE A 376 TYR 0.022 0.001 TYR O 49 ARG 0.014 0.001 ARG B 633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 308 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8726 (t0) cc_final: 0.8411 (t0) REVERT: B 530 MET cc_start: 0.8796 (mmm) cc_final: 0.8575 (mmt) REVERT: C 69 TRP cc_start: 0.8226 (m-90) cc_final: 0.7676 (m-90) REVERT: C 363 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: E 577 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8062 (tm-30) REVERT: E 585 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8250 (mtp-110) REVERT: E 601 LYS cc_start: 0.9185 (mttt) cc_final: 0.8872 (mmmm) REVERT: D 95 MET cc_start: 0.8804 (ptm) cc_final: 0.8485 (ptt) REVERT: F 530 MET cc_start: 0.9218 (mtm) cc_final: 0.8854 (mtt) REVERT: F 574 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8792 (mtmt) REVERT: F 584 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8242 (mt-10) REVERT: F 621 MET cc_start: 0.9255 (tpt) cc_final: 0.8794 (tpt) REVERT: G 100 ASP cc_start: 0.7757 (m-30) cc_final: 0.7520 (t0) REVERT: G 105 GLN cc_start: 0.9070 (pt0) cc_final: 0.8636 (pp30) REVERT: I 82 GLU cc_start: 0.8899 (tt0) cc_final: 0.8413 (tp30) REVERT: H 13 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8698 (mmmt) REVERT: L 2 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5664 (t80) REVERT: L 49 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7528 (t80) REVERT: L 50 GLU cc_start: 0.7756 (pm20) cc_final: 0.7481 (pm20) REVERT: M 56 ASN cc_start: 0.8991 (m-40) cc_final: 0.8438 (t0) REVERT: M 64 LYS cc_start: 0.8620 (tttt) cc_final: 0.8411 (tptt) REVERT: M 77 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8385 (mm-40) REVERT: M 100 MET cc_start: 0.6973 (mtt) cc_final: 0.6553 (ttm) REVERT: J 3 GLN cc_start: 0.7693 (mp10) cc_final: 0.7360 (mp10) REVERT: J 6 GLU cc_start: 0.7831 (mp0) cc_final: 0.7486 (mp0) REVERT: J 12 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8467 (mptt) REVERT: J 31 LYS cc_start: 0.9152 (tppp) cc_final: 0.8907 (tmmt) REVERT: J 52 ASN cc_start: 0.8809 (t0) cc_final: 0.8257 (t0) REVERT: J 86 ASP cc_start: 0.8731 (m-30) cc_final: 0.8478 (m-30) REVERT: J 100 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8557 (mm-30) REVERT: N 94 MET cc_start: 0.8789 (ttt) cc_final: 0.8535 (ttp) REVERT: K 3 GLN cc_start: 0.8635 (tt0) cc_final: 0.8318 (tm-30) REVERT: K 72 ASP cc_start: 0.8098 (t0) cc_final: 0.7524 (t0) outliers start: 58 outliers final: 46 residues processed: 349 average time/residue: 0.3387 time to fit residues: 186.3786 Evaluate side-chains 333 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 GLN O 36 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055754 restraints weight = 105297.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057363 restraints weight = 61882.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058373 restraints weight = 45264.160| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24493 Z= 0.220 Angle : 0.826 43.516 33281 Z= 0.374 Chirality : 0.050 0.356 4172 Planarity : 0.004 0.056 3994 Dihedral : 7.046 59.844 6200 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.34 % Allowed : 18.47 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2731 helix: 1.98 (0.29), residues: 340 sheet: 0.10 (0.18), residues: 879 loop : -0.97 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 34 HIS 0.006 0.001 HIS O 33 PHE 0.018 0.001 PHE A 376 TYR 0.022 0.002 TYR L 30 ARG 0.013 0.000 ARG B 633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4853.11 seconds wall clock time: 89 minutes 18.80 seconds (5358.80 seconds total)