Starting phenix.real_space_refine on Sun Apr 14 22:16:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cdi_7460/04_2024/6cdi_7460_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cdi_7460/04_2024/6cdi_7460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cdi_7460/04_2024/6cdi_7460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cdi_7460/04_2024/6cdi_7460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cdi_7460/04_2024/6cdi_7460_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cdi_7460/04_2024/6cdi_7460_neut.pdb" } resolution = 3.6 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= 0.012 sd= 0.121 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 168 5.16 5 C 20523 2.51 5 N 5316 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "l ARG 108": "NH1" <-> "NH2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 52": "NH1" <-> "NH2" Residue "8 ARG 61": "NH1" <-> "NH2" Residue "4 ARG 108": "NH1" <-> "NH2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32763 Number of models: 1 Model: "" Number of chains: 81 Chain: "c" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "d" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "h" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "l" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "3" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "4" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" 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: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" 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: "i" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "AA" 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: "BA" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "CA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "DA" 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: "EA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "FA" 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: "GA" 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: "HA" 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: "IA" 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: "JA" 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: "KA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "LA" 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: "MA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.87, per 1000 atoms: 0.51 Number of scatterers: 32763 At special positions: 0 Unit cell: (157.29, 160.5, 154.08, 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 168 16.00 O 6756 8.00 N 5316 7.00 C 20523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 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=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.02 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.02 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.04 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=2.02 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 n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 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 N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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 Atom "HETATM30180 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31880 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31030 O5 NAG b 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30230 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31930 O5 NAG 1 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31080 O5 NAG e 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30780 O5 NAG W 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32480 O5 NAGJA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31630 O5 NAG v 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30513 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32213 O5 NAGDA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31363 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32719 O5 NAG A 702 .*. O " rejected from bonding due to valence issues. Atom "HETATM32747 O5 NAG D 702 .*. O " rejected from bonding due to valence issues. Atom "HETATM32691 O5 NAG c 702 .*. O " rejected from bonding due to valence issues. Atom "HETATM30369 O5 NAG J 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32069 O5 NAGBA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31219 O5 NAG i 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30808 O5 NAG X 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31658 O5 NAG w 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32508 O5 NAGKA 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN P 4 " - " MAN P 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN o 4 " - " MAN o 5 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " " MANBA 4 " - " MANBA 5 " " MANBA 5 " - " MANBA 6 " " MANEA 4 " - " MANEA 5 " " MANKA 4 " - " MANKA 5 " " MANKA 5 " - " MANKA 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 9 3 " - " MAN 9 4 " " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 8 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA o 3 " - " MAN o 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " " BMA y 3 " - " MAN y 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " " MANBA 7 " - " MANBA 8 " " BMAEA 3 " - " MANEA 4 " " BMAIA 3 " - " MANIA 4 " " BMAKA 3 " - " MANKA 4 " " MANKA 7 " - " MANKA 8 " " BMAMA 3 " - " MANMA 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 7 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 9 " " BMA g 3 " - " MAN g 5 " " BMA i 3 " - " MAN i 7 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 6 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " " BMAAA 3 " - " MANAA 5 " " BMABA 3 " - " MANBA 7 " " BMACA 3 " - " MANCA 4 " " BMAEA 3 " - " MANEA 6 " " BMAIA 3 " - " MANIA 5 " " BMAKA 3 " - " MANKA 7 " " MANKA 7 " - " MANKA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 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 O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 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 o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " 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 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 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGMA 2 " - " BMAMA 3 " NAG-ASN " NAG 0 1 " - " ASN C 88 " " NAG 1 1 " - " ASN C 133 " " NAG 2 644 " - " ASN 2 355 " " NAG 9 1 " - " ASN C 137 " " NAG A 702 " - " ASN A 637 " " NAG B 1 " - " ASN c 611 " " NAG C 644 " - " ASN C 355 " " NAG D 702 " - " ASN D 637 " " NAG E 1 " - " ASN d 88 " " NAG F 1 " - " ASN d 133 " " NAG G 1 " - " ASN d 137 " " NAG I 1 " - " ASN d 156 " " NAG J 1 " - " ASN d 160 " " NAG K 1 " - " ASN d 197 " " NAG O 1 " - " ASN d 234 " " NAG P 1 " - " ASN d 262 " " NAG S 1 " - " ASN d 295 " " NAG T 1 " - " ASN d 301 " " NAG U 1 " - " ASN d 363 " " NAG V 1 " - " ASN d 386 " " NAG W 1 " - " ASN d 392 " " NAG X 1 " - " ASN d 332 " " NAG Y 1 " - " ASN d 448 " " NAG Z 1 " - " ASN d 276 " " NAG a 1 " - " ASN A 611 " " NAG b 1 " - " ASN 2 88 " " NAG c 702 " - " ASN c 637 " " NAG d 644 " - " ASN d 355 " " NAG e 1 " - " ASN 2 133 " " NAG f 1 " - " ASN 2 137 " " NAG g 1 " - " ASN 2 156 " " NAG i 1 " - " ASN 2 160 " " NAG j 1 " - " ASN 2 197 " " NAG k 1 " - " ASN 2 234 " " NAG o 1 " - " ASN 2 262 " " NAG p 1 " - " ASN 2 295 " " NAG s 1 " - " ASN 2 301 " " NAG t 1 " - " ASN 2 363 " " NAG u 1 " - " ASN 2 386 " " NAG v 1 " - " ASN 2 392 " " NAG w 1 " - " ASN 2 332 " " NAG x 1 " - " ASN 2 448 " " NAG y 1 " - " ASN 2 276 " " NAG z 1 " - " ASN D 611 " " NAGAA 1 " - " ASN C 156 " " NAGBA 1 " - " ASN C 160 " " NAGCA 1 " - " ASN C 197 " " NAGDA 1 " - " ASN C 234 " " NAGEA 1 " - " ASN C 262 " " NAGFA 1 " - " ASN C 295 " " NAGGA 1 " - " ASN C 301 " " NAGHA 1 " - " ASN C 363 " " NAGIA 1 " - " ASN C 386 " " NAGJA 1 " - " ASN C 392 " " NAGKA 1 " - " ASN C 332 " " NAGLA 1 " - " ASN C 448 " " NAGMA 1 " - " ASN C 276 " Time building additional restraints: 16.71 Conformation dependent library (CDL) restraints added in 5.9 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 99 sheets defined 13.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'c' and resid 514 through 520 removed outlier: 3.833A pdb=" N VAL c 518 " --> pdb=" O GLY c 514 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 537 through 543 Processing helix chain 'c' and resid 570 through 595 removed outlier: 3.639A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 623 removed outlier: 3.584A pdb=" N ILE c 622 " --> pdb=" O ASN c 618 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.890A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 640 through 664 removed outlier: 3.653A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 63 removed outlier: 3.506A pdb=" N TYR d 61 " --> pdb=" O ASP d 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR d 63 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 115 removed outlier: 3.659A pdb=" N ILE d 109 " --> pdb=" O HIS d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.661A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 198 Processing helix chain 'd' and resid 335 through 350 Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 475 through 481 removed outlier: 3.542A pdb=" N SER d 481 " --> pdb=" O ASP d 477 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.809A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 82 removed outlier: 3.597A pdb=" N PHE r 82 " --> pdb=" O ARG r 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.583A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 520 removed outlier: 3.833A pdb=" N VAL A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.641A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.584A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.889A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 664 removed outlier: 3.654A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 63 removed outlier: 3.506A pdb=" N TYR 2 61 " --> pdb=" O ASP 2 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.659A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 3.662A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 Processing helix chain '2' and resid 475 through 481 removed outlier: 3.543A pdb=" N SER 2 481 " --> pdb=" O ASP 2 477 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.808A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 82 removed outlier: 3.596A pdb=" N PHE 7 82 " --> pdb=" O ARG 7 79 " (cutoff:3.500A) Processing helix chain '8' and resid 61 through 64 removed outlier: 3.583A pdb=" N GLN 8 64 " --> pdb=" O ARG 8 61 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 61 through 64' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.764A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 520 removed outlier: 3.833A pdb=" N VAL D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.640A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.584A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.889A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.653A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.505A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.659A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.661A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.542A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.808A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.597A pdb=" N PHE R 82 " --> pdb=" O ARG R 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.583A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.764A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 603 through 609 removed outlier: 3.513A pdb=" N VAL d 38 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR c 606 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL d 36 " --> pdb=" O THR c 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 45 through 47 removed outlier: 3.879A pdb=" N ILE d 225 " --> pdb=" O VAL d 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR d 244 " --> pdb=" O ILE d 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'd' and resid 91 through 94 removed outlier: 3.892A pdb=" N GLU d 91 " --> pdb=" O CYS d 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.471A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 271 through 273 removed outlier: 7.478A pdb=" N GLN d 293 " --> pdb=" O SER d 334 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER d 334 " --> pdb=" O GLN d 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 271 through 273 removed outlier: 11.176A pdb=" N VAL d 286 " --> pdb=" O THR d 455 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N THR d 455 " --> pdb=" O VAL d 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE d 288 " --> pdb=" O ILE d 453 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N ILE d 453 " --> pdb=" O PHE d 288 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N THR d 290 " --> pdb=" O GLY d 451 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY d 451 " --> pdb=" O THR d 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 302 through 308 removed outlier: 5.530A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 359 through 361 removed outlier: 3.529A pdb=" N ILE d 359 " --> pdb=" O TRP d 395 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER d 393 " --> pdb=" O PHE d 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 374 through 377 removed outlier: 3.833A pdb=" N HIS d 374 " --> pdb=" O CYS d 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'n' and resid 9 through 12 removed outlier: 5.977A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 19 through 23 removed outlier: 3.696A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'm' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'm' and resid 46 through 51 removed outlier: 6.476A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR m 90 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 95 through 96 Processing sheet with id=AC1, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AC2, first strand: chain 'r' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.811A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE q 34 " --> pdb=" O TRP q 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP q 50 " --> pdb=" O ILE q 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP q 36 " --> pdb=" O ILE q 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.811A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 10 through 11 removed outlier: 3.703A pdb=" N GLU h 10 " --> pdb=" O THR h 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS h 38 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP h 47 " --> pdb=" O LYS h 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR h 40 " --> pdb=" O LEU h 45 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU h 45 " --> pdb=" O THR h 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'h' and resid 17 through 18 Processing sheet with id=AD2, first strand: chain 'h' and resid 22 through 23 removed outlier: 3.604A pdb=" N CYS h 22 " --> pdb=" O ALA h 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA h 78 " --> pdb=" O CYS h 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 5 through 7 Processing sheet with id=AD4, first strand: chain 'l' and resid 10 through 12 removed outlier: 3.952A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'l' and resid 35 through 36 removed outlier: 6.443A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'l' and resid 89 through 90 removed outlier: 4.117A pdb=" N THR l 97 " --> pdb=" O GLN l 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.723A pdb=" N THR A 606 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL 2 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL A 608 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '2' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR 2 244 " --> pdb=" O ILE 2 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '2' and resid 55 through 56 Processing sheet with id=AE1, first strand: chain '2' and resid 91 through 94 removed outlier: 3.891A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AE3, first strand: chain '2' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain '2' and resid 202 through 203 removed outlier: 6.471A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.478A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '2' and resid 271 through 273 removed outlier: 11.176A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '2' and resid 302 through 308 removed outlier: 5.529A pdb=" N THR 2 303 " --> pdb=" O GLY 2 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2' and resid 359 through 361 removed outlier: 3.529A pdb=" N ILE 2 359 " --> pdb=" O TRP 2 395 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '2' and resid 374 through 377 removed outlier: 3.834A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '6' and resid 9 through 12 removed outlier: 5.977A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '6' and resid 19 through 23 removed outlier: 3.696A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '5' and resid 6 through 7 Processing sheet with id=AF4, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain '5' and resid 46 through 51 removed outlier: 6.475A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '5' and resid 95 through 96 Processing sheet with id=AF7, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AF8, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AF9, first strand: chain '7' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU 7 11 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '7' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU 7 11 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AG3, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain '8' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE 8 34 " --> pdb=" O TRP 8 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP 8 50 " --> pdb=" O ILE 8 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP 8 36 " --> pdb=" O ILE 8 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '8' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '3' and resid 10 through 11 removed outlier: 3.704A pdb=" N GLU 3 10 " --> pdb=" O THR 3 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY 3 49 " --> pdb=" O TRP 3 36 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS 3 38 " --> pdb=" O TRP 3 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP 3 47 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR 3 40 " --> pdb=" O LEU 3 45 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU 3 45 " --> pdb=" O THR 3 40 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '3' and resid 17 through 18 Processing sheet with id=AG8, first strand: chain '3' and resid 22 through 23 removed outlier: 3.604A pdb=" N CYS 3 22 " --> pdb=" O ALA 3 78 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA 3 78 " --> pdb=" O CYS 3 22 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '4' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain '4' and resid 10 through 12 removed outlier: 3.952A pdb=" N GLY 4 84 " --> pdb=" O LEU 4 104 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '4' and resid 35 through 36 removed outlier: 6.442A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '4' and resid 89 through 90 removed outlier: 4.118A pdb=" N THR 4 97 " --> pdb=" O GLN 4 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 603 through 609 removed outlier: 3.513A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.879A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 244 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AH7, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.891A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AH9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AI1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.471A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.478A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.176A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 302 through 308 removed outlier: 5.529A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.529A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 374 through 377 removed outlier: 3.833A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 9 through 12 removed outlier: 5.977A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.696A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'M' and resid 6 through 7 Processing sheet with id=AJ1, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AJ2, first strand: chain 'M' and resid 46 through 51 removed outlier: 6.475A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR M 90 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR M 105 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 95 through 96 Processing sheet with id=AJ4, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AJ5, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AJ6, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.285A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AJ9, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AK1, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.812A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.703A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AK5, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.604A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AK7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.952A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'L' and resid 35 through 36 removed outlier: 6.442A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'L' and resid 89 through 90 removed outlier: 4.117A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2448 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: 14.26 Time building geometry restraints manager: 17.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9900 1.34 - 1.46: 8773 1.46 - 1.58: 14558 1.58 - 1.70: 9 1.70 - 1.82: 222 Bond restraints: 33462 Sorted by residual: bond pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.399 1.502 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C1 MANBA 4 " pdb=" O5 MANBA 4 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C1 MAN i 4 " pdb=" O5 MAN i 4 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C1 MAN J 4 " pdb=" C2 MAN J 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C1 MANBA 4 " pdb=" C2 MANBA 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.19e+01 ... (remaining 33457 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.19: 883 106.19 - 113.18: 19335 113.18 - 120.16: 11010 120.16 - 127.15: 13767 127.15 - 134.14: 455 Bond angle restraints: 45450 Sorted by residual: angle pdb=" N VAL c 570 " pdb=" CA VAL c 570 " pdb=" C VAL c 570 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" N VAL A 570 " pdb=" CA VAL A 570 " pdb=" C VAL A 570 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" N VAL D 570 " pdb=" CA VAL D 570 " pdb=" C VAL D 570 " ideal model delta sigma weight residual 112.96 106.67 6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" N ILE d 138 " pdb=" CA ILE d 138 " pdb=" C ILE d 138 " ideal model delta sigma weight residual 108.11 116.56 -8.45 1.40e+00 5.10e-01 3.64e+01 angle pdb=" N ILE C 138 " pdb=" CA ILE C 138 " pdb=" C ILE C 138 " ideal model delta sigma weight residual 108.11 116.56 -8.45 1.40e+00 5.10e-01 3.64e+01 ... (remaining 45445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 21282 22.61 - 45.21: 711 45.21 - 67.82: 169 67.82 - 90.42: 203 90.42 - 113.03: 123 Dihedral angle restraints: 22488 sinusoidal: 11484 harmonic: 11004 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -173.23 87.23 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CB CYS d 201 " pdb=" SG CYS d 201 " pdb=" SG CYS d 433 " pdb=" CB CYS d 433 " ideal model delta sinusoidal sigma weight residual -86.00 -173.21 87.21 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS 2 201 " pdb=" SG CYS 2 201 " pdb=" SG CYS 2 433 " pdb=" CB CYS 2 433 " ideal model delta sinusoidal sigma weight residual -86.00 -173.21 87.21 1 1.00e+01 1.00e-02 9.13e+01 ... (remaining 22485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 5619 0.306 - 0.613: 24 0.613 - 0.919: 3 0.919 - 1.226: 12 1.226 - 1.532: 6 Chirality restraints: 5664 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN 2 88 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.86e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN d 88 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.85e+01 ... (remaining 5661 not shown) Planarity restraints: 5520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN d 88 " -0.181 2.00e-02 2.50e+03 4.19e-01 2.20e+03 pdb=" CG ASN d 88 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN d 88 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN d 88 " 0.708 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.559 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 88 " 0.181 2.00e-02 2.50e+03 4.19e-01 2.19e+03 pdb=" CG ASN 2 88 " -0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 88 " 0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 88 " -0.708 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.559 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 88 " -0.181 2.00e-02 2.50e+03 4.19e-01 2.19e+03 pdb=" CG ASN C 88 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN C 88 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN C 88 " 0.708 2.00e-02 2.50e+03 pdb=" C1 NAG 0 1 " -0.558 2.00e-02 2.50e+03 ... (remaining 5517 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 19 2.15 - 2.84: 10453 2.84 - 3.52: 40948 3.52 - 4.21: 74820 4.21 - 4.90: 126169 Nonbonded interactions: 252409 Sorted by model distance: nonbonded pdb=" OG SER n 12 " pdb=" CG1 ILE n 105 " model vdw 1.461 3.440 nonbonded pdb=" OG SER N 12 " pdb=" CG1 ILE N 105 " model vdw 1.461 3.440 nonbonded pdb=" OG SER 6 12 " pdb=" CG1 ILE 6 105 " model vdw 1.462 3.440 nonbonded pdb=" O VAL N 13 " pdb=" O ALA N 14 " model vdw 1.491 3.040 nonbonded pdb=" O VAL 6 13 " pdb=" O ALA 6 14 " model vdw 1.492 3.040 ... (remaining 252404 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 '9' selection = chain 'CA' selection = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'MA' selection = chain 'Z' selection = chain 'b' selection = chain 'f' selection = chain 'j' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain 'F' selection = chain 'FA' selection = chain 'GA' selection = chain 'JA' selection = chain 'LA' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'e' selection = chain 'p' selection = chain 's' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'd' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'c' } ncs_group { reference = chain 'AA' selection = chain 'I' selection = chain 'IA' selection = chain 'V' selection = chain 'g' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'DA' selection = chain 'HA' selection = chain 'O' selection = chain 'U' selection = chain 'a' selection = chain 'k' selection = chain 't' selection = chain 'z' } ncs_group { reference = (chain 'BA' and (resid 1 or resid 4 through 8)) selection = (chain 'J' and (resid 1 or resid 4 through 8)) selection = (chain 'KA' and (resid 2 or resid 5 through 9)) selection = (chain 'X' and (resid 2 or resid 5 through 9)) selection = (chain 'i' and (resid 1 or resid 4 through 8)) selection = (chain 'w' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'EA' selection = chain 'P' selection = chain 'o' } 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.180 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 90.030 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.940 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.008 0.103 33462 Z= 0.480 Angle : 1.062 9.961 45450 Z= 0.523 Chirality : 0.101 1.532 5664 Planarity : 0.006 0.068 5463 Dihedral : 16.867 113.026 15297 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 0.45 % Allowed : 2.98 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -3.25 (0.12), residues: 3777 helix: -2.51 (0.20), residues: 378 sheet: -1.78 (0.14), residues: 1203 loop : -2.36 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP q 103 HIS 0.016 0.003 HIS h 35 PHE 0.028 0.003 PHE d 93 TYR 0.024 0.003 TYR 2 217 ARG 0.008 0.001 ARG d 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 831 time to evaluate : 3.707 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 595 ILE cc_start: 0.9225 (pt) cc_final: 0.8956 (mt) REVERT: c 632 ASP cc_start: 0.8393 (t0) cc_final: 0.8160 (t0) REVERT: c 659 ASP cc_start: 0.7990 (t0) cc_final: 0.7734 (t70) REVERT: m 48 ILE cc_start: 0.9103 (mt) cc_final: 0.8689 (mt) REVERT: m 72 ASP cc_start: 0.8017 (t0) cc_final: 0.6823 (t0) REVERT: m 100 MET cc_start: 0.9224 (mpp) cc_final: 0.8851 (mmm) REVERT: r 32 MET cc_start: 0.8908 (tpp) cc_final: 0.8612 (tpp) REVERT: r 33 THR cc_start: 0.9618 (m) cc_final: 0.9186 (p) REVERT: h 46 ASP cc_start: 0.7682 (m-30) cc_final: 0.7126 (m-30) REVERT: h 60 ASN cc_start: 0.7594 (m-40) cc_final: 0.7062 (p0) REVERT: h 80 MET cc_start: 0.6385 (mmt) cc_final: 0.5659 (tpp) REVERT: h 82 LEU cc_start: 0.8089 (mt) cc_final: 0.7717 (mp) REVERT: h 100 TYR cc_start: 0.8103 (p90) cc_final: 0.7818 (p90) REVERT: l 9 LEU cc_start: 0.8472 (mt) cc_final: 0.8254 (tt) REVERT: l 85 VAL cc_start: 0.7530 (t) cc_final: 0.7202 (t) REVERT: A 659 ASP cc_start: 0.8364 (t0) cc_final: 0.7985 (t70) REVERT: 6 26 GLU cc_start: 0.7517 (tt0) cc_final: 0.7170 (tt0) REVERT: 5 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8237 (tm-30) REVERT: 5 48 ILE cc_start: 0.9155 (mt) cc_final: 0.8869 (mt) REVERT: 5 72 ASP cc_start: 0.7525 (t0) cc_final: 0.6274 (t0) REVERT: 8 63 LEU cc_start: 0.9202 (mp) cc_final: 0.8994 (mt) REVERT: 3 46 ASP cc_start: 0.7536 (m-30) cc_final: 0.5716 (m-30) REVERT: 3 60 ASN cc_start: 0.7530 (m-40) cc_final: 0.6912 (p0) REVERT: 3 80 MET cc_start: 0.6803 (mmt) cc_final: 0.6515 (mmm) REVERT: 3 82 LEU cc_start: 0.7947 (mt) cc_final: 0.7716 (mt) REVERT: 4 11 LEU cc_start: 0.7970 (mt) cc_final: 0.7741 (tp) REVERT: 4 85 VAL cc_start: 0.7941 (t) cc_final: 0.7617 (t) REVERT: D 625 ASN cc_start: 0.7791 (t0) cc_final: 0.7480 (t0) REVERT: D 659 ASP cc_start: 0.8243 (t0) cc_final: 0.7842 (t70) REVERT: N 26 GLU cc_start: 0.7922 (tt0) cc_final: 0.7577 (tt0) REVERT: M 46 GLU cc_start: 0.8647 (tt0) cc_final: 0.8432 (tm-30) REVERT: M 48 ILE cc_start: 0.9255 (mt) cc_final: 0.8979 (mt) REVERT: M 72 ASP cc_start: 0.7941 (t0) cc_final: 0.6823 (t0) REVERT: R 32 MET cc_start: 0.8943 (tpp) cc_final: 0.8365 (tpp) REVERT: Q 76 ASP cc_start: 0.8008 (m-30) cc_final: 0.7722 (m-30) REVERT: Q 87 THR cc_start: 0.9200 (m) cc_final: 0.8959 (p) REVERT: H 80 MET cc_start: 0.6729 (mmt) cc_final: 0.5887 (tpp) REVERT: H 82 LEU cc_start: 0.7982 (mt) cc_final: 0.7499 (mp) REVERT: L 2 VAL cc_start: 0.7581 (t) cc_final: 0.6820 (p) REVERT: L 9 LEU cc_start: 0.8631 (mt) cc_final: 0.8238 (tt) outliers start: 15 outliers final: 7 residues processed: 844 average time/residue: 0.5477 time to fit residues: 685.3477 Evaluate side-chains 452 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 445 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 197 ASN Chi-restraints excluded: chain d residue 448 ASN Chi-restraints excluded: chain 2 residue 197 ASN Chi-restraints excluded: chain 2 residue 448 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 3.9990 chunk 284 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 293 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 340 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 203 GLN d 249 HIS d 302 ASN d 315 GLN d 374 HIS n 42 GLN r 41 GLN q 6 GLN q 101 GLN A 625 ASN ** 2 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 302 ASN 2 315 GLN 2 374 HIS 8 6 GLN 8 101 GLN 3 39 GLN D 651 ASN C 249 HIS C 302 ASN C 315 GLN C 374 HIS Q 6 GLN Q 101 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33462 Z= 0.199 Angle : 0.742 9.469 45450 Z= 0.350 Chirality : 0.049 0.224 5664 Planarity : 0.005 0.058 5463 Dihedral : 15.646 106.967 8383 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.68 % Allowed : 10.90 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -2.40 (0.13), residues: 3777 helix: -1.21 (0.24), residues: 411 sheet: -1.20 (0.14), residues: 1221 loop : -1.93 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 6 96 HIS 0.007 0.001 HIS H 35 PHE 0.016 0.002 PHE n 9 TYR 0.022 0.001 TYR n 87 ARG 0.010 0.001 ARG 3 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 512 time to evaluate : 3.677 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: c 595 ILE cc_start: 0.9302 (pt) cc_final: 0.8926 (mt) REVERT: c 632 ASP cc_start: 0.8394 (t0) cc_final: 0.8177 (t0) REVERT: c 648 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7981 (tp30) REVERT: c 657 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8026 (mm-30) REVERT: d 139 THR cc_start: 0.6032 (OUTLIER) cc_final: 0.5774 (p) REVERT: d 475 MET cc_start: 0.8657 (tpt) cc_final: 0.8263 (mmt) REVERT: n 26 GLU cc_start: 0.8458 (tt0) cc_final: 0.8241 (tt0) REVERT: n 87 TYR cc_start: 0.7890 (m-10) cc_final: 0.7380 (m-80) REVERT: m 46 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7546 (tm-30) REVERT: m 48 ILE cc_start: 0.8818 (mt) cc_final: 0.8570 (mt) REVERT: r 4 LEU cc_start: 0.9109 (mt) cc_final: 0.8855 (mm) REVERT: r 32 MET cc_start: 0.8819 (tpp) cc_final: 0.8595 (tpt) REVERT: r 33 THR cc_start: 0.9584 (m) cc_final: 0.9155 (p) REVERT: h 33 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7926 (mm-30) REVERT: h 48 ILE cc_start: 0.8848 (mm) cc_final: 0.8555 (mp) REVERT: h 60 ASN cc_start: 0.7323 (m-40) cc_final: 0.6883 (p0) REVERT: h 80 MET cc_start: 0.6289 (mmt) cc_final: 0.6024 (tpp) REVERT: l 9 LEU cc_start: 0.8386 (mt) cc_final: 0.8154 (tt) REVERT: l 30 ASP cc_start: 0.7980 (p0) cc_final: 0.7667 (p0) REVERT: A 608 VAL cc_start: 0.9500 (OUTLIER) cc_final: 0.9295 (m) REVERT: A 657 GLU cc_start: 0.8614 (tp30) cc_final: 0.8410 (tp30) REVERT: 2 125 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9231 (tt) REVERT: 6 26 GLU cc_start: 0.7721 (tt0) cc_final: 0.7503 (tt0) REVERT: 5 46 GLU cc_start: 0.8699 (tt0) cc_final: 0.8481 (tm-30) REVERT: 4 11 LEU cc_start: 0.7851 (mt) cc_final: 0.7642 (tp) REVERT: 4 54 ARG cc_start: 0.7694 (ptp90) cc_final: 0.7410 (ptp90) REVERT: 4 85 VAL cc_start: 0.7467 (t) cc_final: 0.6885 (t) REVERT: D 659 ASP cc_start: 0.7945 (t0) cc_final: 0.7712 (t70) REVERT: N 17 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8329 (mp10) REVERT: N 25 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6127 (pp20) REVERT: N 105 ILE cc_start: 0.6965 (pt) cc_final: 0.6691 (pt) REVERT: M 46 GLU cc_start: 0.8820 (tt0) cc_final: 0.8588 (tm-30) REVERT: R 32 MET cc_start: 0.8844 (tpp) cc_final: 0.8519 (tpp) REVERT: Q 61 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7796 (ttm-80) REVERT: Q 76 ASP cc_start: 0.8064 (m-30) cc_final: 0.7709 (t0) REVERT: Q 87 THR cc_start: 0.9169 (m) cc_final: 0.8925 (p) REVERT: H 80 MET cc_start: 0.6653 (mmt) cc_final: 0.6253 (mmm) REVERT: H 82 LEU cc_start: 0.7617 (mt) cc_final: 0.7414 (mp) REVERT: L 9 LEU cc_start: 0.8591 (mt) cc_final: 0.8184 (tt) REVERT: L 79 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8077 (mp0) outliers start: 89 outliers final: 53 residues processed: 568 average time/residue: 0.5127 time to fit residues: 445.6719 Evaluate side-chains 485 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 426 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 69 TRP Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 434 MET Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 4 residue 4 MET Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 303 optimal weight: 0.4980 chunk 338 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 103 GLN ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN 2 203 GLN 2 249 HIS 5 23 ASN ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 64 GLN ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 ASN ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 64 GLN L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 33462 Z= 0.379 Angle : 0.761 12.859 45450 Z= 0.363 Chirality : 0.049 0.226 5664 Planarity : 0.005 0.058 5463 Dihedral : 13.598 113.283 8370 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.91 % Allowed : 10.81 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -2.01 (0.13), residues: 3777 helix: -0.33 (0.26), residues: 411 sheet: -1.04 (0.14), residues: 1200 loop : -1.73 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP h 47 HIS 0.006 0.001 HIS m 52 PHE 0.027 0.002 PHE 2 288 TYR 0.022 0.002 TYR L 87 ARG 0.012 0.001 ARG 4 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 440 time to evaluate : 3.656 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: c 595 ILE cc_start: 0.9373 (pt) cc_final: 0.9081 (mt) REVERT: c 657 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8033 (mm-30) REVERT: m 46 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7837 (tm-30) REVERT: r 4 LEU cc_start: 0.9138 (mt) cc_final: 0.8901 (mm) REVERT: r 33 THR cc_start: 0.9654 (m) cc_final: 0.9188 (p) REVERT: h 60 ASN cc_start: 0.7257 (m-40) cc_final: 0.7024 (p0) REVERT: l 9 LEU cc_start: 0.8429 (mt) cc_final: 0.8203 (tt) REVERT: l 34 GLU cc_start: 0.7036 (mp0) cc_final: 0.6807 (mp0) REVERT: 2 125 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9325 (tt) REVERT: 5 46 GLU cc_start: 0.8765 (tt0) cc_final: 0.8450 (tm-30) REVERT: 3 33 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8015 (mm-30) REVERT: 3 46 ASP cc_start: 0.7041 (m-30) cc_final: 0.6722 (m-30) REVERT: 3 48 ILE cc_start: 0.8575 (mt) cc_final: 0.8344 (mm) REVERT: 3 80 MET cc_start: 0.7242 (mmm) cc_final: 0.5982 (mmm) REVERT: 4 54 ARG cc_start: 0.7836 (ptp90) cc_final: 0.7624 (ptp90) REVERT: D 648 GLU cc_start: 0.8458 (tp30) cc_final: 0.8194 (tp30) REVERT: D 659 ASP cc_start: 0.7956 (t0) cc_final: 0.7678 (t70) REVERT: M 46 GLU cc_start: 0.8883 (tt0) cc_final: 0.8576 (tm-30) REVERT: M 100 MET cc_start: 0.9130 (mpp) cc_final: 0.8173 (mpp) REVERT: R 32 MET cc_start: 0.8956 (tpp) cc_final: 0.8549 (tpp) REVERT: Q 87 THR cc_start: 0.9244 (m) cc_final: 0.9002 (p) REVERT: H 48 ILE cc_start: 0.8763 (mm) cc_final: 0.8360 (mp) REVERT: L 9 LEU cc_start: 0.8526 (mt) cc_final: 0.8195 (tp) REVERT: L 50 LYS cc_start: 0.7632 (tppt) cc_final: 0.7255 (ttpt) REVERT: L 79 GLU cc_start: 0.8166 (mp0) cc_final: 0.7823 (mp0) REVERT: L 82 ASP cc_start: 0.6549 (m-30) cc_final: 0.6208 (m-30) outliers start: 130 outliers final: 86 residues processed: 527 average time/residue: 0.5059 time to fit residues: 407.9183 Evaluate side-chains 486 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 399 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 583 VAL Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 637 ASN Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 103 GLN Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 114 GLN Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 27 TYR Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 385 CYS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 434 MET Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 80 MET Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 2 VAL Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 97 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 177 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 362 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 103 GLN ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 88 GLN C 203 GLN M 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33462 Z= 0.186 Angle : 0.670 10.082 45450 Z= 0.315 Chirality : 0.046 0.242 5664 Planarity : 0.004 0.058 5463 Dihedral : 11.848 110.475 8370 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.43 % Allowed : 12.47 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3777 helix: 0.17 (0.27), residues: 414 sheet: -0.89 (0.14), residues: 1263 loop : -1.49 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 96 HIS 0.005 0.001 HIS m 52 PHE 0.018 0.001 PHE 8 100D TYR 0.019 0.001 TYR 4 87 ARG 0.007 0.001 ARG 6 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 441 time to evaluate : 3.750 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: c 595 ILE cc_start: 0.9337 (pt) cc_final: 0.9048 (mt) REVERT: c 657 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8059 (mm-30) REVERT: m 46 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7053 (tm-30) REVERT: r 4 LEU cc_start: 0.9066 (mt) cc_final: 0.8817 (mm) REVERT: r 33 THR cc_start: 0.9546 (m) cc_final: 0.9118 (p) REVERT: h 48 ILE cc_start: 0.8858 (mm) cc_final: 0.8361 (mp) REVERT: h 80 MET cc_start: 0.7344 (mmm) cc_final: 0.6103 (mmm) REVERT: l 9 LEU cc_start: 0.8394 (mt) cc_final: 0.8164 (tt) REVERT: l 34 GLU cc_start: 0.7091 (mp0) cc_final: 0.6868 (mp0) REVERT: l 105 GLU cc_start: 0.4058 (OUTLIER) cc_final: 0.3696 (tt0) REVERT: 2 125 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9371 (tt) REVERT: 5 46 GLU cc_start: 0.8790 (tt0) cc_final: 0.8498 (tm-30) REVERT: 7 33 THR cc_start: 0.9650 (m) cc_final: 0.9208 (p) REVERT: 8 87 THR cc_start: 0.9216 (m) cc_final: 0.8972 (p) REVERT: 3 33 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7942 (mm-30) REVERT: 3 80 MET cc_start: 0.7138 (mmm) cc_final: 0.5941 (mmm) REVERT: 4 34 GLU cc_start: 0.6903 (mp0) cc_final: 0.6574 (mp0) REVERT: 4 36 TYR cc_start: 0.7135 (m-10) cc_final: 0.6687 (m-10) REVERT: D 648 GLU cc_start: 0.8401 (tp30) cc_final: 0.8126 (tp30) REVERT: D 659 ASP cc_start: 0.7877 (t0) cc_final: 0.7643 (t70) REVERT: C 125 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9217 (tt) REVERT: M 46 GLU cc_start: 0.8848 (tt0) cc_final: 0.8524 (tm-30) REVERT: R 32 MET cc_start: 0.8816 (tpp) cc_final: 0.8483 (tpp) REVERT: H 29 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7201 (t80) REVERT: H 48 ILE cc_start: 0.8694 (mm) cc_final: 0.8376 (mp) REVERT: H 80 MET cc_start: 0.7190 (mmm) cc_final: 0.5745 (mmm) REVERT: L 9 LEU cc_start: 0.8573 (mt) cc_final: 0.8245 (tp) REVERT: L 79 GLU cc_start: 0.8030 (mp0) cc_final: 0.7680 (mp0) REVERT: L 82 ASP cc_start: 0.6626 (m-30) cc_final: 0.6251 (m-30) outliers start: 114 outliers final: 80 residues processed: 515 average time/residue: 0.5290 time to fit residues: 421.9261 Evaluate side-chains 475 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 391 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 636 SER Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 114 GLN Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 7 residue 88 GLN Chi-restraints excluded: chain 8 residue 80 MET Chi-restraints excluded: chain 3 residue 27 TYR Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 58 ASN Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 293 GLN ** d 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 GLN q 64 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 33462 Z= 0.509 Angle : 0.798 13.184 45450 Z= 0.381 Chirality : 0.050 0.248 5664 Planarity : 0.005 0.059 5463 Dihedral : 11.713 115.222 8370 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.40 % Allowed : 12.89 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 3777 helix: -0.05 (0.26), residues: 423 sheet: -0.85 (0.14), residues: 1236 loop : -1.53 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 96 HIS 0.005 0.001 HIS 2 330 PHE 0.033 0.003 PHE 2 288 TYR 0.021 0.002 TYR 4 87 ARG 0.008 0.001 ARG 4 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 394 time to evaluate : 3.556 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: c 595 ILE cc_start: 0.9425 (pt) cc_final: 0.9175 (mt) REVERT: c 657 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8139 (mm-30) REVERT: d 125 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9263 (tt) REVERT: d 139 THR cc_start: 0.6647 (OUTLIER) cc_final: 0.6283 (p) REVERT: n 87 TYR cc_start: 0.8120 (m-80) cc_final: 0.6955 (m-10) REVERT: h 48 ILE cc_start: 0.8890 (mm) cc_final: 0.8459 (mp) REVERT: h 80 MET cc_start: 0.7505 (mmm) cc_final: 0.6425 (mmm) REVERT: l 9 LEU cc_start: 0.8483 (mt) cc_final: 0.8271 (tt) REVERT: l 105 GLU cc_start: 0.4052 (OUTLIER) cc_final: 0.3649 (tt0) REVERT: 2 125 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9393 (tt) REVERT: 2 475 MET cc_start: 0.8689 (mmm) cc_final: 0.8052 (mmt) REVERT: 5 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8519 (tm-30) REVERT: 5 73 LYS cc_start: 0.7920 (tppt) cc_final: 0.7667 (tppt) REVERT: 8 100 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: 3 33 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8019 (mm-30) REVERT: 3 46 ASP cc_start: 0.7104 (m-30) cc_final: 0.6548 (m-30) REVERT: 3 80 MET cc_start: 0.7124 (mmm) cc_final: 0.6091 (mmm) REVERT: D 648 GLU cc_start: 0.8491 (tp30) cc_final: 0.8199 (tp30) REVERT: D 659 ASP cc_start: 0.8028 (t0) cc_final: 0.7798 (t70) REVERT: M 46 GLU cc_start: 0.8914 (tt0) cc_final: 0.8425 (tm-30) REVERT: R 32 MET cc_start: 0.8997 (tpp) cc_final: 0.8618 (tpp) REVERT: Q 1 GLN cc_start: 0.8636 (pm20) cc_final: 0.8412 (pm20) REVERT: H 29 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7458 (t80) REVERT: H 48 ILE cc_start: 0.8718 (mm) cc_final: 0.8326 (mp) REVERT: L 9 LEU cc_start: 0.8611 (mt) cc_final: 0.8315 (tp) outliers start: 146 outliers final: 95 residues processed: 494 average time/residue: 0.5084 time to fit residues: 387.1293 Evaluate side-chains 466 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 365 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 620 SER Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 637 ASN Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 110 SER Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 80 MET Chi-restraints excluded: chain 8 residue 83 THR Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 4 residue 27 VAL Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 97 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 58 ASN Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 9.9990 chunk 326 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 362 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 293 GLN m 23 ASN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33462 Z= 0.192 Angle : 0.678 11.295 45450 Z= 0.321 Chirality : 0.046 0.250 5664 Planarity : 0.004 0.059 5463 Dihedral : 10.721 109.723 8370 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.73 % Allowed : 13.97 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3777 helix: 0.44 (0.27), residues: 420 sheet: -0.62 (0.15), residues: 1224 loop : -1.40 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 338 HIS 0.003 0.001 HIS M 52 PHE 0.020 0.001 PHE 3 98 TYR 0.026 0.001 TYR N 87 ARG 0.015 0.001 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 398 time to evaluate : 3.718 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: c 595 ILE cc_start: 0.9351 (pt) cc_final: 0.9122 (mt) REVERT: d 125 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9211 (tt) REVERT: d 139 THR cc_start: 0.6406 (OUTLIER) cc_final: 0.6024 (p) REVERT: n 87 TYR cc_start: 0.8076 (m-80) cc_final: 0.7036 (m-10) REVERT: r 33 THR cc_start: 0.9595 (m) cc_final: 0.9096 (p) REVERT: h 29 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6697 (t80) REVERT: h 48 ILE cc_start: 0.8838 (mm) cc_final: 0.8407 (mp) REVERT: h 80 MET cc_start: 0.7523 (mmm) cc_final: 0.6563 (mmm) REVERT: l 9 LEU cc_start: 0.8504 (mt) cc_final: 0.8272 (tt) REVERT: l 105 GLU cc_start: 0.4017 (OUTLIER) cc_final: 0.3591 (tt0) REVERT: A 588 ARG cc_start: 0.8374 (ttm170) cc_final: 0.7633 (mtm180) REVERT: 2 125 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9415 (tt) REVERT: 2 475 MET cc_start: 0.8576 (mmm) cc_final: 0.7849 (mmt) REVERT: 5 46 GLU cc_start: 0.8819 (tt0) cc_final: 0.8493 (tm-30) REVERT: 8 87 THR cc_start: 0.9253 (m) cc_final: 0.9037 (p) REVERT: 3 33 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7943 (mm-30) REVERT: 3 46 ASP cc_start: 0.7040 (m-30) cc_final: 0.6457 (m-30) REVERT: 3 80 MET cc_start: 0.6888 (mmm) cc_final: 0.6132 (mmm) REVERT: 4 36 TYR cc_start: 0.7133 (m-10) cc_final: 0.6811 (m-10) REVERT: D 648 GLU cc_start: 0.8406 (tp30) cc_final: 0.8113 (tp30) REVERT: D 659 ASP cc_start: 0.7944 (t0) cc_final: 0.7733 (t70) REVERT: M 46 GLU cc_start: 0.8893 (tt0) cc_final: 0.8420 (tm-30) REVERT: R 32 MET cc_start: 0.8806 (tpp) cc_final: 0.8475 (tpp) REVERT: R 49 ASP cc_start: 0.8120 (t0) cc_final: 0.7784 (t0) REVERT: Q 1 GLN cc_start: 0.8638 (pm20) cc_final: 0.8374 (pm20) REVERT: H 29 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7223 (t80) REVERT: H 48 ILE cc_start: 0.8681 (mm) cc_final: 0.8207 (mp) REVERT: H 80 MET cc_start: 0.7238 (mmm) cc_final: 0.6209 (mmm) REVERT: L 9 LEU cc_start: 0.8623 (mt) cc_final: 0.8330 (tp) outliers start: 124 outliers final: 77 residues processed: 483 average time/residue: 0.5051 time to fit residues: 378.2034 Evaluate side-chains 457 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 374 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 636 SER Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 423 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 29 PHE Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 28 ASP Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 80 MET Chi-restraints excluded: chain 3 residue 27 TYR Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 361 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 41 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** 2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33462 Z= 0.336 Angle : 0.711 9.681 45450 Z= 0.337 Chirality : 0.047 0.252 5664 Planarity : 0.005 0.102 5463 Dihedral : 10.464 111.938 8370 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.52 % Allowed : 14.84 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3777 helix: 0.61 (0.27), residues: 405 sheet: -0.45 (0.15), residues: 1194 loop : -1.43 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 50 HIS 0.003 0.001 HIS M 52 PHE 0.022 0.002 PHE H 98 TYR 0.018 0.001 TYR N 87 ARG 0.012 0.001 ARG 4 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 373 time to evaluate : 3.414 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: c 595 ILE cc_start: 0.9410 (pt) cc_final: 0.9180 (mt) REVERT: c 632 ASP cc_start: 0.8593 (t0) cc_final: 0.8381 (t0) REVERT: d 125 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9248 (tt) REVERT: d 139 THR cc_start: 0.6173 (OUTLIER) cc_final: 0.5821 (p) REVERT: n 87 TYR cc_start: 0.8194 (m-80) cc_final: 0.7110 (m-80) REVERT: r 33 THR cc_start: 0.9607 (m) cc_final: 0.9141 (p) REVERT: h 29 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6826 (t80) REVERT: h 48 ILE cc_start: 0.8885 (mm) cc_final: 0.8464 (mp) REVERT: h 80 MET cc_start: 0.7424 (mmm) cc_final: 0.6436 (mmm) REVERT: l 9 LEU cc_start: 0.8595 (mt) cc_final: 0.8385 (tt) REVERT: l 105 GLU cc_start: 0.4167 (OUTLIER) cc_final: 0.3743 (tt0) REVERT: 2 475 MET cc_start: 0.8643 (mmm) cc_final: 0.7950 (mmt) REVERT: 5 46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8509 (tm-30) REVERT: 8 87 THR cc_start: 0.9299 (m) cc_final: 0.9079 (p) REVERT: 3 33 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7867 (mm-30) REVERT: 3 46 ASP cc_start: 0.7119 (m-30) cc_final: 0.6505 (m-30) REVERT: 3 80 MET cc_start: 0.6925 (mmm) cc_final: 0.6214 (mmm) REVERT: 4 79 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7205 (pp20) REVERT: D 648 GLU cc_start: 0.8421 (tp30) cc_final: 0.8136 (tp30) REVERT: D 659 ASP cc_start: 0.7972 (t0) cc_final: 0.7761 (t70) REVERT: C 271 MET cc_start: 0.8723 (mmt) cc_final: 0.8405 (mmt) REVERT: M 46 GLU cc_start: 0.8900 (tt0) cc_final: 0.8395 (tm-30) REVERT: R 32 MET cc_start: 0.8896 (tpp) cc_final: 0.8580 (tpp) REVERT: Q 1 GLN cc_start: 0.8742 (pm20) cc_final: 0.8465 (pm20) REVERT: H 29 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7545 (t80) REVERT: H 80 MET cc_start: 0.7341 (mmm) cc_final: 0.6276 (mmm) REVERT: L 4 MET cc_start: 0.7443 (mmm) cc_final: 0.7215 (mmm) REVERT: L 9 LEU cc_start: 0.8664 (mt) cc_final: 0.8371 (tp) REVERT: L 105 GLU cc_start: 0.4214 (OUTLIER) cc_final: 0.3767 (tt0) outliers start: 117 outliers final: 90 residues processed: 457 average time/residue: 0.4889 time to fit residues: 346.4228 Evaluate side-chains 454 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 358 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 423 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 59 ASP Chi-restraints excluded: chain q residue 63 LEU Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 29 PHE Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 80 MET Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 246 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 103 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33462 Z= 0.279 Angle : 0.692 9.526 45450 Z= 0.328 Chirality : 0.046 0.259 5664 Planarity : 0.004 0.055 5463 Dihedral : 10.046 110.939 8370 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.40 % Allowed : 15.21 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3777 helix: 0.75 (0.27), residues: 405 sheet: -0.41 (0.15), residues: 1224 loop : -1.34 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 50 HIS 0.004 0.001 HIS M 52 PHE 0.021 0.002 PHE 3 98 TYR 0.021 0.001 TYR N 87 ARG 0.014 0.001 ARG 4 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 376 time to evaluate : 3.667 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: c 543 ASN cc_start: 0.8693 (t0) cc_final: 0.8451 (t0) REVERT: c 595 ILE cc_start: 0.9397 (pt) cc_final: 0.9187 (mt) REVERT: c 632 ASP cc_start: 0.8580 (t0) cc_final: 0.8368 (t0) REVERT: d 125 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9232 (tt) REVERT: d 139 THR cc_start: 0.6281 (OUTLIER) cc_final: 0.5914 (p) REVERT: n 87 TYR cc_start: 0.8143 (m-80) cc_final: 0.7184 (m-80) REVERT: r 33 THR cc_start: 0.9592 (m) cc_final: 0.9121 (p) REVERT: h 29 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6785 (t80) REVERT: h 46 ASP cc_start: 0.7839 (m-30) cc_final: 0.7382 (m-30) REVERT: h 48 ILE cc_start: 0.8884 (mm) cc_final: 0.8349 (mp) REVERT: h 80 MET cc_start: 0.7572 (mmm) cc_final: 0.6599 (mmm) REVERT: l 9 LEU cc_start: 0.8607 (mt) cc_final: 0.8388 (tt) REVERT: l 105 GLU cc_start: 0.4096 (OUTLIER) cc_final: 0.3667 (tt0) REVERT: 2 475 MET cc_start: 0.8626 (mmm) cc_final: 0.7917 (mmt) REVERT: 5 46 GLU cc_start: 0.8848 (tt0) cc_final: 0.8503 (tm-30) REVERT: 8 87 THR cc_start: 0.9292 (m) cc_final: 0.9071 (p) REVERT: 3 33 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7889 (mm-30) REVERT: 3 46 ASP cc_start: 0.7047 (m-30) cc_final: 0.6434 (m-30) REVERT: 3 80 MET cc_start: 0.6883 (mmm) cc_final: 0.6307 (mmm) REVERT: 4 79 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7226 (pp20) REVERT: D 648 GLU cc_start: 0.8431 (tp30) cc_final: 0.8140 (tp30) REVERT: D 659 ASP cc_start: 0.7970 (t0) cc_final: 0.7768 (t70) REVERT: M 46 GLU cc_start: 0.8883 (tt0) cc_final: 0.8403 (tm-30) REVERT: R 32 MET cc_start: 0.8844 (tpp) cc_final: 0.8554 (tpp) REVERT: Q 1 GLN cc_start: 0.8804 (pm20) cc_final: 0.8514 (pm20) REVERT: H 48 ILE cc_start: 0.8553 (mm) cc_final: 0.8154 (mp) REVERT: H 80 MET cc_start: 0.7205 (mmm) cc_final: 0.6300 (mmm) REVERT: L 4 MET cc_start: 0.7439 (mmm) cc_final: 0.7234 (mmm) REVERT: L 9 LEU cc_start: 0.8661 (mt) cc_final: 0.8377 (tp) REVERT: L 78 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7721 (p) REVERT: L 105 GLU cc_start: 0.4209 (OUTLIER) cc_final: 0.3750 (tt0) outliers start: 113 outliers final: 93 residues processed: 459 average time/residue: 0.4996 time to fit residues: 356.1495 Evaluate side-chains 458 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 359 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 538 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 103 GLN Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 271 MET Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 423 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 29 PHE Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 28 ASP Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 80 MET Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 97 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 4.9990 chunk 346 optimal weight: 0.0870 chunk 315 optimal weight: 7.9990 chunk 336 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 304 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 103 GLN ** h 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33462 Z= 0.248 Angle : 0.708 13.141 45450 Z= 0.336 Chirality : 0.047 0.448 5664 Planarity : 0.004 0.064 5463 Dihedral : 9.743 110.127 8370 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.19 % Allowed : 15.69 % Favored : 81.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3777 helix: 0.82 (0.28), residues: 405 sheet: -0.26 (0.15), residues: 1209 loop : -1.32 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 50 HIS 0.003 0.001 HIS M 52 PHE 0.023 0.002 PHE q 91 TYR 0.020 0.001 TYR N 87 ARG 0.014 0.001 ARG 4 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 373 time to evaluate : 3.739 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: c 543 ASN cc_start: 0.8728 (t0) cc_final: 0.8476 (t0) REVERT: c 632 ASP cc_start: 0.8562 (t0) cc_final: 0.8344 (t0) REVERT: d 125 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9221 (tt) REVERT: d 139 THR cc_start: 0.6297 (OUTLIER) cc_final: 0.5931 (p) REVERT: n 87 TYR cc_start: 0.8014 (m-80) cc_final: 0.7176 (m-80) REVERT: r 33 THR cc_start: 0.9576 (m) cc_final: 0.9110 (p) REVERT: h 29 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6785 (t80) REVERT: h 46 ASP cc_start: 0.7899 (m-30) cc_final: 0.7425 (m-30) REVERT: h 48 ILE cc_start: 0.8768 (mm) cc_final: 0.8342 (mp) REVERT: h 80 MET cc_start: 0.7543 (mmm) cc_final: 0.6579 (mmm) REVERT: l 4 MET cc_start: 0.7262 (mmm) cc_final: 0.6856 (mmm) REVERT: l 9 LEU cc_start: 0.8600 (mt) cc_final: 0.8383 (tt) REVERT: l 37 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8675 (pp) REVERT: l 105 GLU cc_start: 0.4094 (OUTLIER) cc_final: 0.3653 (tt0) REVERT: 5 46 GLU cc_start: 0.8842 (tt0) cc_final: 0.8497 (tm-30) REVERT: 8 87 THR cc_start: 0.9284 (m) cc_final: 0.9066 (p) REVERT: 3 33 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7911 (mm-30) REVERT: 3 43 ARG cc_start: 0.7277 (mtm-85) cc_final: 0.6447 (ptt-90) REVERT: 3 46 ASP cc_start: 0.7075 (m-30) cc_final: 0.6476 (m-30) REVERT: 3 80 MET cc_start: 0.6853 (mmm) cc_final: 0.6330 (mmm) REVERT: 3 82 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6551 (mmt90) REVERT: 4 79 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7186 (pp20) REVERT: D 530 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8062 (ptm) REVERT: D 648 GLU cc_start: 0.8409 (tp30) cc_final: 0.8125 (tp30) REVERT: M 46 GLU cc_start: 0.8872 (tt0) cc_final: 0.8396 (tm-30) REVERT: R 32 MET cc_start: 0.8812 (tpp) cc_final: 0.8532 (tpp) REVERT: R 49 ASP cc_start: 0.8300 (t0) cc_final: 0.7886 (t0) REVERT: Q 1 GLN cc_start: 0.8831 (pm20) cc_final: 0.8535 (pm20) REVERT: H 46 ASP cc_start: 0.7624 (m-30) cc_final: 0.7083 (m-30) REVERT: H 48 ILE cc_start: 0.8593 (mm) cc_final: 0.8193 (mp) REVERT: H 80 MET cc_start: 0.7198 (mmm) cc_final: 0.6400 (mmm) REVERT: L 9 LEU cc_start: 0.8698 (mt) cc_final: 0.8410 (tp) REVERT: L 78 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7873 (p) REVERT: L 105 GLU cc_start: 0.4239 (OUTLIER) cc_final: 0.3773 (tt0) outliers start: 106 outliers final: 86 residues processed: 451 average time/residue: 0.4974 time to fit residues: 349.0680 Evaluate side-chains 460 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 365 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 423 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 59 ASP Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 29 PHE Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 28 ASP Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 370 GLU Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 82 ARG Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 97 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.4980 chunk 356 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 247 optimal weight: 7.9990 chunk 373 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 229 optimal weight: 9.9990 chunk 182 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 575 GLN h 1 GLN ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33462 Z= 0.204 Angle : 0.688 13.758 45450 Z= 0.325 Chirality : 0.046 0.247 5664 Planarity : 0.004 0.063 5463 Dihedral : 9.157 108.461 8370 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.80 % Allowed : 16.11 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.95 (0.14), residues: 3777 helix: 1.00 (0.28), residues: 405 sheet: -0.19 (0.15), residues: 1224 loop : -1.24 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 112 HIS 0.003 0.001 HIS M 52 PHE 0.027 0.001 PHE q 91 TYR 0.017 0.001 TYR N 87 ARG 0.014 0.001 ARG 4 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 384 time to evaluate : 3.785 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: c 543 ASN cc_start: 0.8750 (t0) cc_final: 0.8488 (t0) REVERT: d 125 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9197 (tt) REVERT: d 139 THR cc_start: 0.6276 (OUTLIER) cc_final: 0.5844 (p) REVERT: n 87 TYR cc_start: 0.7984 (m-80) cc_final: 0.7174 (m-80) REVERT: r 33 THR cc_start: 0.9541 (m) cc_final: 0.9009 (p) REVERT: h 46 ASP cc_start: 0.7862 (m-30) cc_final: 0.7438 (m-30) REVERT: h 80 MET cc_start: 0.7539 (mmm) cc_final: 0.6537 (mmm) REVERT: l 9 LEU cc_start: 0.8600 (mt) cc_final: 0.8387 (tt) REVERT: l 37 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (pp) REVERT: l 105 GLU cc_start: 0.4124 (OUTLIER) cc_final: 0.3717 (tt0) REVERT: 5 46 GLU cc_start: 0.8829 (tt0) cc_final: 0.8449 (tm-30) REVERT: 7 33 THR cc_start: 0.9645 (m) cc_final: 0.9217 (p) REVERT: 8 87 THR cc_start: 0.9272 (m) cc_final: 0.9051 (p) REVERT: 3 33 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7858 (mm-30) REVERT: 3 43 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6470 (ptt-90) REVERT: 3 46 ASP cc_start: 0.6946 (m-30) cc_final: 0.6352 (m-30) REVERT: 3 80 MET cc_start: 0.6949 (mmm) cc_final: 0.6454 (mmm) REVERT: 3 82 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6513 (mmt90) REVERT: 4 4 MET cc_start: 0.7413 (mmm) cc_final: 0.7197 (mmm) REVERT: 4 61 ARG cc_start: 0.5855 (ptt90) cc_final: 0.5264 (ptt180) REVERT: 4 77 ARG cc_start: 0.7235 (tmm160) cc_final: 0.6839 (tpt90) REVERT: 4 79 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7102 (pp20) REVERT: D 530 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8033 (ptm) REVERT: D 648 GLU cc_start: 0.8388 (tp30) cc_final: 0.8110 (tp30) REVERT: M 46 GLU cc_start: 0.8865 (tt0) cc_final: 0.8377 (tm-30) REVERT: R 32 MET cc_start: 0.8746 (tpp) cc_final: 0.8487 (tpp) REVERT: R 49 ASP cc_start: 0.8121 (t0) cc_final: 0.7800 (t0) REVERT: Q 1 GLN cc_start: 0.8847 (pm20) cc_final: 0.8541 (pm20) REVERT: H 46 ASP cc_start: 0.7708 (m-30) cc_final: 0.7164 (m-30) REVERT: H 48 ILE cc_start: 0.8643 (mm) cc_final: 0.8254 (mp) REVERT: H 80 MET cc_start: 0.7304 (mmm) cc_final: 0.6539 (mmm) REVERT: L 9 LEU cc_start: 0.8754 (mt) cc_final: 0.8475 (tp) REVERT: L 105 GLU cc_start: 0.4180 (OUTLIER) cc_final: 0.3697 (tt0) outliers start: 93 outliers final: 77 residues processed: 455 average time/residue: 0.5010 time to fit residues: 355.5391 Evaluate side-chains 455 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 371 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 604 CYS Chi-restraints excluded: chain c residue 659 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 111 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 201 CYS Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 272 ILE Chi-restraints excluded: chain d residue 374 HIS Chi-restraints excluded: chain d residue 385 CYS Chi-restraints excluded: chain d residue 416 LEU Chi-restraints excluded: chain d residue 423 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 59 ASP Chi-restraints excluded: chain q residue 100 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 28 ASP Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 105 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 75 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 242 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 272 ILE Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 45 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 82 ARG Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 97 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 297 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 305 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.081025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056975 restraints weight = 105639.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.058793 restraints weight = 58225.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.059912 restraints weight = 42332.272| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33462 Z= 0.206 Angle : 0.782 57.330 45450 Z= 0.390 Chirality : 0.047 0.359 5664 Planarity : 0.005 0.111 5463 Dihedral : 9.108 108.366 8370 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.74 % Allowed : 16.71 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.89 (0.14), residues: 3777 helix: 1.08 (0.28), residues: 402 sheet: -0.13 (0.15), residues: 1224 loop : -1.21 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP q 54 HIS 0.003 0.001 HIS M 52 PHE 0.025 0.001 PHE q 91 TYR 0.020 0.001 TYR 8 32 ARG 0.017 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7549.87 seconds wall clock time: 139 minutes 18.18 seconds (8358.18 seconds total)