Starting phenix.real_space_refine on Sat Feb 17 06:03:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fae_28954/02_2024/8fae_28954_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 96 5.16 5 C 10949 2.51 5 N 2663 2.21 5 O 3985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E ARG 469": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17693 Number of models: 1 Model: "" Number of chains: 79 Chain: "B" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1157 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 1, 'TRANS': 143} Chain: "C" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3675 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "E" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3675 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Chain: "A" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3684 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 22, 'TRANS': 445} Chain breaks: 1 Chain: "F" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1143 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain: "G" 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: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "OA" 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: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 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: "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: 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: "v" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "w" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 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: "3" 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: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 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: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 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: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "AA" 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: "BA" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "CA" 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: "DA" 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: "EA" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "HA" 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: "IA" 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: "JA" 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: "KA" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "LA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "MA" 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: "NA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 9.71, per 1000 atoms: 0.55 Number of scatterers: 17693 At special positions: 0 Unit cell: (146.85, 146.85, 133.65, 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 96 16.00 O 3985 8.00 N 2663 7.00 C 10949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 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=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN X 4 " - " MAN X 5 " " MAN v 4 " - " MAN v 5 " " MANEA 4 " - " MANEA 5 " " MANOA 4 " - " MANOA 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " BMA 9 3 " - " MAN 9 7 " " MAN 9 4 " - " MAN 9 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA k 3 " - " MAN k 4 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " " BMADA 3 " - " MANDA 4 " " BMAEA 3 " - " MANEA 4 " " BMAGA 3 " - " MANGA 4 " " BMAHA 3 " - " MANHA 4 " " BMAOA 3 " - " MANOA 4 " " MANOA 6 " - " MANOA 7 " ALPHA1-6 " BMA 9 3 " - " MAN 9 4 " " MAN 9 4 " - " MAN 9 6 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 7 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 5 " " BMA u 3 " - " MAN u 4 " " BMA v 3 " - " MAN v 6 " " MAN v 6 " - " MAN v 7 " " BMA y 3 " - " MAN y 4 " " BMAEA 3 " - " MANEA 6 " " MANEA 6 " - " MANEA 7 " " BMAHA 3 " - " MANHA 5 " " BMAOA 3 " - " MANOA 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " BMA o 3 " - " NAG o 4 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " NAGBA 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 " " NAGGA 2 " - " BMAGA 3 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGOA 2 " - " BMAOA 3 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 3 " " NAG O 1 " - " FUC O 3 " " NAG Y 1 " - " FUC Y 2 " " NAG e 1 " - " FUC e 4 " " NAG f 1 " - " FUC f 3 " " NAG g 1 " - " FUC g 3 " " NAG m 1 " - " FUC m 3 " " NAG z 1 " - " FUC z 4 " " NAGKA 1 " - " FUCKA 4 " " NAGLA 1 " - " FUCLA 3 " " NAGNA 1 " - " FUCNA 3 " NAG-ASN " NAG 0 1 " - " ASN E 448 " " NAG 1 1 " - " ASN A 88 " " NAG 2 1 " - " ASN A 130 " " NAG 3 1 " - " ASN A 156 " " NAG 4 1 " - " ASN A 160 " " NAG 5 1 " - " ASN A 188 " " NAG 6 1 " - " ASN A 197 " " NAG 7 1 " - " ASN A 234 " " NAG 8 1 " - " ASN A 241 " " NAG 9 1 " - " ASN A 262 " " NAG A 602 " - " ASN A 356 " " NAG C 602 " - " ASN C 397 " " NAG E 602 " - " ASN E 356 " " NAG G 1 " - " ASN B 611 " " NAG H 1 " - " ASN B 616 " " NAG I 1 " - " ASN B 625 " " NAG J 1 " - " ASN B 637 " " NAG K 1 " - " ASN C 88 " " NAG L 1 " - " ASN C 130 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 197 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 241 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 301 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN C 339 " " NAG Y 1 " - " ASN C 356 " " NAG Z 1 " - " ASN C 362 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 392 " " NAG c 1 " - " ASN C 401 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN D 611 " " NAG f 1 " - " ASN D 616 " " NAG g 1 " - " ASN D 625 " " NAG h 1 " - " ASN D 637 " " NAG i 1 " - " ASN E 88 " " NAG j 1 " - " ASN E 130 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 188 " " NAG n 1 " - " ASN E 197 " " NAG o 1 " - " ASN E 234 " " NAG p 1 " - " ASN E 241 " " NAG r 1 " - " ASN E 276 " " NAG s 1 " - " ASN E 295 " " NAG t 1 " - " ASN E 301 " " NAG u 1 " - " ASN E 332 " " NAG v 1 " - " ASN E 339 " " NAG w 1 " - " ASN E 362 " " NAG x 1 " - " ASN E 386 " " NAG y 1 " - " ASN E 392 " " NAG z 1 " - " ASN E 401 " " NAGAA 1 " - " ASN A 276 " " NAGBA 1 " - " ASN A 295 " " NAGCA 1 " - " ASN A 301 " " NAGDA 1 " - " ASN A 332 " " NAGEA 1 " - " ASN A 339 " " NAGFA 1 " - " ASN A 362 " " NAGGA 1 " - " ASN A 386 " " NAGHA 1 " - " ASN A 392 " " NAGIA 1 " - " ASN A 401 " " NAGJA 1 " - " ASN A 448 " " NAGKA 1 " - " ASN F 611 " " NAGLA 1 " - " ASN F 616 " " NAGMA 1 " - " ASN F 625 " " NAGNA 1 " - " ASN F 637 " " NAGOA 1 " - " ASN E 262 " Time building additional restraints: 11.89 Conformation dependent library (CDL) restraints added in 2.8 seconds 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 28 sheets defined 26.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'B' and resid 537 through 563 removed outlier: 3.760A pdb=" N ASN B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.697A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 663 removed outlier: 5.716A pdb=" N GLY B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU B 648 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN B 650 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN B 651 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.516A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 475 through 485 removed outlier: 4.047A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 526 No H-bonds generated for 'chain 'D' and resid 524 through 526' Processing helix chain 'D' and resid 530 through 535 Processing helix chain 'D' and resid 537 through 562 removed outlier: 3.933A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 561 " --> pdb=" O LYS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 4.024A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 628 through 634 removed outlier: 3.842A pdb=" N LYS D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 660 removed outlier: 4.606A pdb=" N GLY D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 352 Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 407 through 410 No H-bonds generated for 'chain 'E' and resid 407 through 410' Processing helix chain 'E' and resid 475 through 483 Processing helix chain 'A' and resid 58 through 64 removed outlier: 4.898A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.676A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 526 No H-bonds generated for 'chain 'F' and resid 524 through 526' Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.136A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 544 removed outlier: 3.589A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 551 No H-bonds generated for 'chain 'F' and resid 548 through 551' Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 660 removed outlier: 4.133A pdb=" N LYS F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP F 636 " --> pdb=" O GLU F 632 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY F 640 " --> pdb=" O ASP F 636 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.542A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= C, first strand: chain 'C' and resid 157 through 159 Processing sheet with id= D, first strand: chain 'C' and resid 201 through 203 removed outlier: 7.184A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.638A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.733A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 306 through 308 Processing sheet with id= H, first strand: chain 'C' and resid 383 through 385 Processing sheet with id= I, first strand: chain 'E' and resid 44 through 47 removed outlier: 4.181A pdb=" N VAL E 44 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'E' and resid 92 through 94 Processing sheet with id= L, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= M, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.734A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= O, first strand: chain 'E' and resid 443 through 449 removed outlier: 3.742A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.900A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 306 through 308 Processing sheet with id= R, first strand: chain 'E' and resid 358 through 360 Processing sheet with id= S, first strand: chain 'E' and resid 375 through 378 Processing sheet with id= T, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= U, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= V, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= W, first strand: chain 'A' and resid 157 through 161 Processing sheet with id= X, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= Y, first strand: chain 'A' and resid 271 through 274 Processing sheet with id= Z, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.716A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 374 through 378 Processing sheet with id= AB, first strand: chain 'A' and resid 301 through 308 removed outlier: 4.002A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1251 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: 5.47 Time building geometry restraints manager: 12.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3337 1.33 - 1.45: 4760 1.45 - 1.57: 9756 1.57 - 1.69: 9 1.69 - 1.81: 132 Bond restraints: 17994 Sorted by residual: bond pdb=" C23 83G C 601 " pdb=" N19 83G C 601 " ideal model delta sigma weight residual 1.477 1.339 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C23 83G A 601 " pdb=" N19 83G A 601 " ideal model delta sigma weight residual 1.477 1.339 0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C23 83G E 601 " pdb=" N19 83G E 601 " ideal model delta sigma weight residual 1.477 1.343 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C14 83G C 601 " pdb=" N16 83G C 601 " ideal model delta sigma weight residual 1.473 1.344 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C14 83G E 601 " pdb=" N16 83G E 601 " ideal model delta sigma weight residual 1.473 1.347 0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 17989 not shown) Histogram of bond angle deviations from ideal: 97.44 - 105.44: 325 105.44 - 113.44: 11588 113.44 - 121.44: 8670 121.44 - 129.45: 3724 129.45 - 137.45: 142 Bond angle restraints: 24449 Sorted by residual: angle pdb=" C10 83G A 601 " pdb=" C11 83G A 601 " pdb=" C12 83G A 601 " ideal model delta sigma weight residual 88.71 125.39 -36.68 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C10 83G C 601 " pdb=" C11 83G C 601 " pdb=" C12 83G C 601 " ideal model delta sigma weight residual 88.71 125.05 -36.34 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C10 83G E 601 " pdb=" C11 83G E 601 " pdb=" C12 83G E 601 " ideal model delta sigma weight residual 88.71 124.59 -35.88 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C08 83G A 601 " pdb=" C11 83G A 601 " pdb=" C12 83G A 601 " ideal model delta sigma weight residual 161.60 128.75 32.85 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C08 83G C 601 " pdb=" C11 83G C 601 " pdb=" C12 83G C 601 " ideal model delta sigma weight residual 161.60 128.82 32.78 3.00e+00 1.11e-01 1.19e+02 ... (remaining 24444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 12245 22.10 - 44.20: 911 44.20 - 66.29: 227 66.29 - 88.39: 259 88.39 - 110.49: 279 Dihedral angle restraints: 13921 sinusoidal: 8623 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 9.52 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 158.04 -65.04 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.49 54.49 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 13918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 3312 0.219 - 0.439: 181 0.439 - 0.658: 12 0.658 - 0.877: 5 0.877 - 1.097: 4 Chirality restraints: 3514 Sorted by residual: chirality pdb=" C1 NAG 6 2 " pdb=" O4 NAG 6 1 " pdb=" C2 NAG 6 2 " pdb=" O5 NAG 6 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.32e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.95e+02 chirality pdb=" C1 BMA 4 3 " pdb=" O4 NAG 4 2 " pdb=" C2 BMA 4 3 " pdb=" O5 BMA 4 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.66e+02 ... (remaining 3511 not shown) Planarity restraints: 2797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 2 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG 6 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG 6 2 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG 6 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG 6 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG o 2 " 0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG o 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG o 2 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG o 2 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG o 2 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG i 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.143 2.00e-02 2.50e+03 ... (remaining 2794 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2160 2.76 - 3.30: 18141 3.30 - 3.83: 29042 3.83 - 4.37: 37378 4.37 - 4.90: 55612 Nonbonded interactions: 142333 Sorted by model distance: nonbonded pdb=" O6 MANOA 6 " pdb=" C1 MANOA 8 " model vdw 2.228 3.470 nonbonded pdb=" O ARG D 579 " pdb=" OG1 THR D 582 " model vdw 2.249 2.440 nonbonded pdb=" N CYS C 378 " pdb=" O GLU C 381 " model vdw 2.312 2.520 nonbonded pdb=" O ILE A 225 " pdb=" OG1 THR A 244 " model vdw 2.318 2.440 nonbonded pdb=" OE1 GLU A 211 " pdb=" O3 NAG 9 1 " model vdw 2.328 2.440 ... (remaining 142328 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' and resid 1 through 2) selection = (chain '1' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '4' and resid 1 through 2) selection = (chain '6' and resid 1 through 2) selection = (chain '8' and resid 1 through 2) selection = (chain 'BA' and resid 1 through 2) selection = (chain 'CA' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'IA' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'JA' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'LA' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'NA' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) } ncs_group { reference = (chain '3' and resid 1 through 3) selection = (chain 'AA' and resid 1 through 3) selection = (chain 'DA' and resid 1 through 3) selection = (chain 'GA' and resid 1 through 3) selection = (chain 'KA' and resid 1 through 3) selection = (chain 'a' and resid 1 through 3) selection = (chain 'e' and resid 1 through 3) selection = (chain 'o' and resid 1 through 3) selection = (chain 'u' and resid 1 through 3) selection = (chain 'w' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) selection = (chain 'z' and resid 1 through 3) } ncs_group { reference = (chain '5' and resid 1) selection = (chain '7' and resid 1) selection = (chain 'FA' and resid 1) selection = (chain 'MA' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'l' and resid 1) } ncs_group { reference = (chain '9' and resid 5 through 7) selection = (chain 'EA' and resid 5 through 7) selection = (chain 'OA' and resid 6 through 8) selection = (chain 'S' and resid 4 through 6) selection = (chain 'X' and resid 5 through 7) selection = (chain 'v' and resid 5 through 7) } ncs_group { reference = (chain 'A' and (resid 33 through 505 or resid 601 through 602)) selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 520 through 661) selection = chain 'D' selection = (chain 'F' and resid 520 through 661) } ncs_group { reference = chain 'HA' selection = chain 'T' selection = chain 'W' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.080 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 53.580 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 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 : 0.013 0.138 17994 Z= 0.795 Angle : 1.724 36.675 24449 Z= 1.060 Chirality : 0.121 1.097 3514 Planarity : 0.035 0.295 2724 Dihedral : 24.786 110.488 10401 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % Rotamer: Outliers : 5.71 % Allowed : 9.52 % Favored : 84.77 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1814 helix: 0.06 (0.25), residues: 466 sheet: -1.44 (0.27), residues: 326 loop : -1.61 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 395 HIS 0.005 0.001 HIS C 216 PHE 0.023 0.002 PHE C 383 TYR 0.017 0.002 TYR E 173 ARG 0.005 0.001 ARG C 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 436 time to evaluate : 2.035 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: B 530 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6426 (ptm) REVERT: B 580 VAL cc_start: 0.9321 (t) cc_final: 0.8617 (t) REVERT: B 584 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 589 ASP cc_start: 0.9416 (m-30) cc_final: 0.9009 (m-30) REVERT: B 595 ILE cc_start: 0.9230 (mm) cc_final: 0.8989 (mm) REVERT: B 605 THR cc_start: 0.9133 (p) cc_final: 0.8791 (t) REVERT: B 630 GLU cc_start: 0.9544 (mt-10) cc_final: 0.9043 (mt-10) REVERT: B 634 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8965 (mp0) REVERT: B 649 SER cc_start: 0.8867 (p) cc_final: 0.8529 (p) REVERT: B 651 ASN cc_start: 0.8818 (m-40) cc_final: 0.8234 (m110) REVERT: C 66 HIS cc_start: 0.8255 (m-70) cc_final: 0.7801 (m90) REVERT: C 97 LYS cc_start: 0.9418 (mptt) cc_final: 0.9044 (mmtm) REVERT: C 107 ASP cc_start: 0.8379 (m-30) cc_final: 0.8149 (m-30) REVERT: C 109 ILE cc_start: 0.9363 (mt) cc_final: 0.8960 (mm) REVERT: C 233 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8006 (t80) REVERT: C 255 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 279 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7979 (p0) REVERT: C 342 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9124 (mt) REVERT: C 359 ILE cc_start: 0.9081 (mp) cc_final: 0.8799 (mm) REVERT: C 373 MET cc_start: 0.7583 (mtp) cc_final: 0.7030 (ttp) REVERT: C 425 ASN cc_start: 0.9209 (m-40) cc_final: 0.9004 (t0) REVERT: C 447 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7963 (t) REVERT: D 523 LEU cc_start: 0.8287 (mt) cc_final: 0.7810 (pp) REVERT: D 627 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8564 (t) REVERT: D 630 GLU cc_start: 0.9090 (pt0) cc_final: 0.8544 (pt0) REVERT: D 648 GLU cc_start: 0.9102 (pp20) cc_final: 0.8871 (pp20) REVERT: D 650 GLN cc_start: 0.9306 (tp40) cc_final: 0.8775 (tm-30) REVERT: D 654 GLU cc_start: 0.8894 (tp30) cc_final: 0.8527 (tp30) REVERT: E 57 ASP cc_start: 0.8006 (t0) cc_final: 0.7452 (p0) REVERT: E 80 ASN cc_start: 0.9249 (p0) cc_final: 0.9041 (t0) REVERT: E 86 LEU cc_start: 0.9765 (mp) cc_final: 0.9509 (mp) REVERT: E 120 VAL cc_start: 0.8969 (t) cc_final: 0.8763 (t) REVERT: E 172 ASP cc_start: 0.8539 (m-30) cc_final: 0.8329 (m-30) REVERT: E 318 TYR cc_start: 0.8406 (m-10) cc_final: 0.8133 (m-80) REVERT: E 381 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: E 393 SER cc_start: 0.7054 (OUTLIER) cc_final: 0.6540 (p) REVERT: E 403 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8273 (p) REVERT: E 475 MET cc_start: 0.7994 (mmm) cc_final: 0.7516 (mmp) REVERT: E 491 ILE cc_start: 0.9559 (mt) cc_final: 0.9297 (mp) REVERT: E 492 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7431 (pm20) REVERT: E 500 LYS cc_start: 0.8218 (mtpp) cc_final: 0.8011 (mmtt) REVERT: A 35 TRP cc_start: 0.8604 (m100) cc_final: 0.8347 (m100) REVERT: A 98 ASN cc_start: 0.8855 (t0) cc_final: 0.8575 (t0) REVERT: A 104 MET cc_start: 0.7999 (ppp) cc_final: 0.7736 (ppp) REVERT: A 107 ASP cc_start: 0.8684 (m-30) cc_final: 0.8448 (m-30) REVERT: A 210 PHE cc_start: 0.8405 (m-80) cc_final: 0.7856 (m-80) REVERT: A 229 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7783 (tptp) REVERT: A 240 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (ttpt) REVERT: A 279 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: A 342 LEU cc_start: 0.8535 (mt) cc_final: 0.8015 (mt) REVERT: A 349 LEU cc_start: 0.9299 (mt) cc_final: 0.9091 (mt) REVERT: A 377 ASN cc_start: 0.8644 (p0) cc_final: 0.8417 (t0) REVERT: A 381 GLU cc_start: 0.7959 (mm-30) cc_final: 0.6949 (mt-10) REVERT: A 383 PHE cc_start: 0.8394 (m-10) cc_final: 0.8128 (m-10) REVERT: A 477 ASP cc_start: 0.9277 (m-30) cc_final: 0.8979 (m-30) REVERT: F 538 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.8943 (t) REVERT: F 539 VAL cc_start: 0.9587 (t) cc_final: 0.9358 (p) REVERT: F 546 SER cc_start: 0.7250 (p) cc_final: 0.6744 (p) REVERT: F 579 ARG cc_start: 0.8716 (mtp85) cc_final: 0.7796 (mmm-85) REVERT: F 580 VAL cc_start: 0.9299 (t) cc_final: 0.8801 (m) REVERT: F 589 ASP cc_start: 0.8954 (m-30) cc_final: 0.8537 (m-30) REVERT: F 618 THR cc_start: 0.8904 (p) cc_final: 0.8392 (t) REVERT: F 626 MET cc_start: 0.8373 (tpt) cc_final: 0.6944 (tpp) REVERT: F 629 MET cc_start: 0.9095 (mmm) cc_final: 0.8243 (tpt) REVERT: F 647 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8614 (mt-10) REVERT: F 648 GLU cc_start: 0.9180 (pp20) cc_final: 0.8907 (pp20) outliers start: 93 outliers final: 20 residues processed: 505 average time/residue: 0.3098 time to fit residues: 230.0288 Evaluate side-chains 295 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 261 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN D 563 GLN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 624 ASN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS A 105 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN F 562 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17994 Z= 0.308 Angle : 0.981 12.944 24449 Z= 0.428 Chirality : 0.060 1.098 3514 Planarity : 0.005 0.045 2724 Dihedral : 19.753 115.632 6976 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.50 % Favored : 93.27 % Rotamer: Outliers : 4.98 % Allowed : 16.28 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1814 helix: 0.04 (0.23), residues: 448 sheet: -1.11 (0.25), residues: 414 loop : -1.31 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP F 571 HIS 0.007 0.001 HIS C 105 PHE 0.015 0.001 PHE E 382 TYR 0.022 0.002 TYR E 173 ARG 0.006 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 249 time to evaluate : 1.819 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: B 530 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6471 (ptm) REVERT: B 584 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8409 (mp0) REVERT: B 589 ASP cc_start: 0.9382 (m-30) cc_final: 0.9049 (m-30) REVERT: B 605 THR cc_start: 0.9087 (p) cc_final: 0.8809 (t) REVERT: B 629 MET cc_start: 0.8365 (tpp) cc_final: 0.8068 (tpp) REVERT: B 630 GLU cc_start: 0.9489 (mt-10) cc_final: 0.8983 (mt-10) REVERT: B 634 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8903 (mp0) REVERT: B 655 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8369 (mmmm) REVERT: C 66 HIS cc_start: 0.8328 (m-70) cc_final: 0.7973 (m90) REVERT: C 95 MET cc_start: 0.8852 (ptt) cc_final: 0.8475 (ppp) REVERT: C 104 MET cc_start: 0.9115 (ttt) cc_final: 0.8849 (tmm) REVERT: C 233 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.9009 (t80) REVERT: C 373 MET cc_start: 0.7951 (mtp) cc_final: 0.6937 (ttm) REVERT: C 430 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8273 (m) REVERT: D 523 LEU cc_start: 0.7651 (mt) cc_final: 0.7137 (pp) REVERT: D 588 ARG cc_start: 0.8626 (ptt90) cc_final: 0.8067 (ptt-90) REVERT: D 615 SER cc_start: 0.9265 (t) cc_final: 0.8831 (p) REVERT: D 626 MET cc_start: 0.7015 (tpp) cc_final: 0.6335 (tpp) REVERT: D 647 GLU cc_start: 0.9617 (pp20) cc_final: 0.9150 (pp20) REVERT: D 648 GLU cc_start: 0.9227 (pp20) cc_final: 0.8952 (pp20) REVERT: E 57 ASP cc_start: 0.8017 (t0) cc_final: 0.7436 (p0) REVERT: E 80 ASN cc_start: 0.9268 (p0) cc_final: 0.8995 (t0) REVERT: E 86 LEU cc_start: 0.9736 (mp) cc_final: 0.9463 (mp) REVERT: E 381 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7065 (mt-10) REVERT: E 434 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7697 (tmm) REVERT: E 475 MET cc_start: 0.8484 (mmm) cc_final: 0.7928 (mmm) REVERT: E 477 ASP cc_start: 0.9275 (m-30) cc_final: 0.8841 (m-30) REVERT: A 35 TRP cc_start: 0.8804 (m100) cc_final: 0.8538 (m100) REVERT: A 36 VAL cc_start: 0.9258 (t) cc_final: 0.8984 (p) REVERT: A 98 ASN cc_start: 0.8936 (t0) cc_final: 0.8603 (t0) REVERT: A 104 MET cc_start: 0.7989 (ppp) cc_final: 0.7627 (ppp) REVERT: A 123 THR cc_start: 0.9256 (p) cc_final: 0.8950 (t) REVERT: A 229 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7686 (tptp) REVERT: A 240 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8771 (ptmm) REVERT: A 360 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8647 (m) REVERT: A 381 GLU cc_start: 0.8179 (mm-30) cc_final: 0.6798 (mt-10) REVERT: A 383 PHE cc_start: 0.8646 (m-10) cc_final: 0.8029 (m-10) REVERT: F 522 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7542 (t80) REVERT: F 538 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.8964 (t) REVERT: F 574 LYS cc_start: 0.9281 (mttp) cc_final: 0.9050 (mttt) REVERT: F 579 ARG cc_start: 0.9016 (mtp85) cc_final: 0.8555 (mmm-85) REVERT: F 583 VAL cc_start: 0.9324 (t) cc_final: 0.9058 (p) REVERT: F 589 ASP cc_start: 0.8980 (m-30) cc_final: 0.8591 (m-30) REVERT: F 601 LYS cc_start: 0.6450 (mtmm) cc_final: 0.5919 (mtmm) REVERT: F 621 MET cc_start: 0.8218 (tpp) cc_final: 0.7848 (tpp) outliers start: 81 outliers final: 43 residues processed: 308 average time/residue: 0.2967 time to fit residues: 136.9150 Evaluate side-chains 263 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 567 LYS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 280 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17994 Z= 0.320 Angle : 0.886 12.119 24449 Z= 0.390 Chirality : 0.054 0.625 3514 Planarity : 0.004 0.051 2724 Dihedral : 14.798 112.386 6950 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 4.79 % Allowed : 19.04 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.06 % 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: -1.24 (0.19), residues: 1814 helix: 0.14 (0.23), residues: 461 sheet: -0.95 (0.25), residues: 399 loop : -1.22 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 596 HIS 0.003 0.001 HIS D 564 PHE 0.013 0.001 PHE A 468 TYR 0.016 0.002 TYR F 586 ARG 0.008 0.001 ARG E 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 219 time to evaluate : 1.826 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: B 530 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.6945 (ptp) REVERT: B 554 ASN cc_start: 0.8907 (m-40) cc_final: 0.8380 (p0) REVERT: B 560 GLU cc_start: 0.8390 (tp30) cc_final: 0.7913 (tm-30) REVERT: B 566 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6663 (pp) REVERT: B 584 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8325 (mt-10) REVERT: B 589 ASP cc_start: 0.9389 (m-30) cc_final: 0.9034 (m-30) REVERT: B 605 THR cc_start: 0.9103 (p) cc_final: 0.8804 (t) REVERT: B 626 MET cc_start: 0.7358 (tpp) cc_final: 0.7012 (tpp) REVERT: B 630 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9118 (mt-10) REVERT: B 633 LYS cc_start: 0.9371 (mtpp) cc_final: 0.9133 (ttmm) REVERT: B 634 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8939 (mp0) REVERT: C 66 HIS cc_start: 0.8383 (m-70) cc_final: 0.8085 (m90) REVERT: C 95 MET cc_start: 0.9091 (ptt) cc_final: 0.8286 (ppp) REVERT: C 185 ASP cc_start: 0.8561 (m-30) cc_final: 0.8315 (t0) REVERT: C 342 LEU cc_start: 0.9519 (mt) cc_final: 0.9315 (mt) REVERT: C 423 ILE cc_start: 0.9084 (mt) cc_final: 0.8795 (pt) REVERT: C 426 MET cc_start: 0.8820 (tpp) cc_final: 0.8356 (mmm) REVERT: D 523 LEU cc_start: 0.8043 (mt) cc_final: 0.7563 (pp) REVERT: D 557 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8878 (pptt) REVERT: D 575 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8689 (pp30) REVERT: D 588 ARG cc_start: 0.8658 (ptt90) cc_final: 0.8243 (ptt-90) REVERT: D 614 TRP cc_start: 0.8560 (m-10) cc_final: 0.7973 (m-90) REVERT: D 615 SER cc_start: 0.8973 (t) cc_final: 0.8710 (p) REVERT: D 626 MET cc_start: 0.7170 (tpp) cc_final: 0.6381 (tpp) REVERT: D 627 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8034 (t) REVERT: D 630 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8794 (pt0) REVERT: D 634 GLU cc_start: 0.8623 (pm20) cc_final: 0.8404 (pm20) REVERT: D 647 GLU cc_start: 0.9568 (pp20) cc_final: 0.9195 (pp20) REVERT: D 648 GLU cc_start: 0.9189 (pp20) cc_final: 0.8897 (pp20) REVERT: E 57 ASP cc_start: 0.7962 (t0) cc_final: 0.7424 (p0) REVERT: E 80 ASN cc_start: 0.9305 (p0) cc_final: 0.9052 (t0) REVERT: E 381 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7205 (mt-10) REVERT: E 434 MET cc_start: 0.8372 (ttt) cc_final: 0.7546 (tmm) REVERT: E 477 ASP cc_start: 0.9257 (m-30) cc_final: 0.8840 (m-30) REVERT: A 35 TRP cc_start: 0.9015 (m100) cc_final: 0.8596 (m100) REVERT: A 123 THR cc_start: 0.9296 (p) cc_final: 0.9041 (t) REVERT: A 240 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (mmtm) REVERT: A 291 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 381 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7389 (mt-10) REVERT: A 383 PHE cc_start: 0.9019 (m-10) cc_final: 0.8432 (m-10) REVERT: F 522 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7457 (t80) REVERT: F 574 LYS cc_start: 0.9301 (mttp) cc_final: 0.9040 (mttt) REVERT: F 579 ARG cc_start: 0.9090 (mtp85) cc_final: 0.8453 (mmm-85) REVERT: F 583 VAL cc_start: 0.9328 (t) cc_final: 0.9047 (p) REVERT: F 589 ASP cc_start: 0.9048 (m-30) cc_final: 0.8603 (m-30) REVERT: F 601 LYS cc_start: 0.6562 (mtmm) cc_final: 0.5986 (mtmm) REVERT: F 621 MET cc_start: 0.8280 (tpp) cc_final: 0.7689 (tpt) REVERT: F 635 ILE cc_start: 0.9362 (mm) cc_final: 0.9087 (mp) REVERT: F 639 THR cc_start: 0.9386 (t) cc_final: 0.9033 (p) REVERT: F 643 TYR cc_start: 0.9093 (m-10) cc_final: 0.8762 (m-10) outliers start: 78 outliers final: 45 residues processed: 277 average time/residue: 0.3101 time to fit residues: 127.1045 Evaluate side-chains 253 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 199 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 596 TRP Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17994 Z= 0.185 Angle : 0.778 9.830 24449 Z= 0.340 Chirality : 0.051 0.534 3514 Planarity : 0.003 0.040 2724 Dihedral : 12.662 100.888 6939 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 3.38 % Allowed : 20.52 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1814 helix: 0.24 (0.24), residues: 453 sheet: -0.79 (0.25), residues: 416 loop : -1.13 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 610 HIS 0.006 0.001 HIS C 105 PHE 0.010 0.001 PHE A 468 TYR 0.015 0.001 TYR D 586 ARG 0.006 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 239 time to evaluate : 1.915 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: B 530 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: B 554 ASN cc_start: 0.9087 (m-40) cc_final: 0.8525 (p0) REVERT: B 560 GLU cc_start: 0.8374 (tp30) cc_final: 0.8000 (tm-30) REVERT: B 584 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 589 ASP cc_start: 0.9352 (m-30) cc_final: 0.8990 (m-30) REVERT: B 605 THR cc_start: 0.9062 (p) cc_final: 0.8723 (t) REVERT: B 626 MET cc_start: 0.7398 (tpp) cc_final: 0.7092 (tpp) REVERT: B 630 GLU cc_start: 0.9497 (mt-10) cc_final: 0.8953 (mt-10) REVERT: B 633 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9113 (ttmm) REVERT: B 634 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8888 (mp0) REVERT: B 659 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 66 HIS cc_start: 0.8392 (m-70) cc_final: 0.8079 (m90) REVERT: C 95 MET cc_start: 0.9066 (ptt) cc_final: 0.8211 (ppp) REVERT: C 185 ASP cc_start: 0.8524 (m-30) cc_final: 0.8274 (t0) REVERT: C 373 MET cc_start: 0.7864 (mtp) cc_final: 0.7019 (ptm) REVERT: C 381 GLU cc_start: 0.8506 (tp30) cc_final: 0.8248 (tp30) REVERT: C 423 ILE cc_start: 0.9095 (mt) cc_final: 0.8871 (pt) REVERT: C 469 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7775 (mtp85) REVERT: D 557 LYS cc_start: 0.9196 (ttpp) cc_final: 0.8827 (pptt) REVERT: D 588 ARG cc_start: 0.8593 (ptt90) cc_final: 0.8222 (ptt-90) REVERT: D 591 GLN cc_start: 0.9171 (mt0) cc_final: 0.8949 (mt0) REVERT: D 614 TRP cc_start: 0.8570 (m-10) cc_final: 0.7916 (m-90) REVERT: D 626 MET cc_start: 0.7019 (tpp) cc_final: 0.6505 (tpp) REVERT: D 627 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8229 (t) REVERT: D 647 GLU cc_start: 0.9556 (pp20) cc_final: 0.9228 (pp20) REVERT: D 648 GLU cc_start: 0.9087 (pp20) cc_final: 0.8806 (pp20) REVERT: E 57 ASP cc_start: 0.7833 (t0) cc_final: 0.7356 (p0) REVERT: E 80 ASN cc_start: 0.9286 (p0) cc_final: 0.9059 (t0) REVERT: E 95 MET cc_start: 0.9368 (ppp) cc_final: 0.8942 (ppp) REVERT: E 104 MET cc_start: 0.9201 (ttm) cc_final: 0.8925 (ttt) REVERT: E 381 GLU cc_start: 0.7904 (mt-10) cc_final: 0.6986 (mt-10) REVERT: E 426 MET cc_start: 0.8121 (mmt) cc_final: 0.7502 (mmm) REVERT: E 434 MET cc_start: 0.8195 (ttt) cc_final: 0.7438 (tmm) REVERT: E 477 ASP cc_start: 0.9157 (m-30) cc_final: 0.8777 (m-30) REVERT: E 492 GLU cc_start: 0.8195 (tp30) cc_final: 0.7990 (tm-30) REVERT: A 35 TRP cc_start: 0.8789 (m100) cc_final: 0.8278 (m100) REVERT: A 123 THR cc_start: 0.9272 (p) cc_final: 0.9034 (t) REVERT: A 150 MET cc_start: 0.4502 (mtm) cc_final: 0.4033 (mtm) REVERT: A 151 ARG cc_start: 0.7486 (mpt180) cc_final: 0.7236 (mmt180) REVERT: A 240 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (mmtm) REVERT: A 381 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7363 (mt-10) REVERT: A 383 PHE cc_start: 0.9024 (m-10) cc_final: 0.8451 (m-10) REVERT: F 522 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7369 (t80) REVERT: F 571 TRP cc_start: 0.8943 (m100) cc_final: 0.8553 (m100) REVERT: F 579 ARG cc_start: 0.9093 (mtp85) cc_final: 0.8389 (mmm-85) REVERT: F 583 VAL cc_start: 0.9294 (t) cc_final: 0.8940 (p) REVERT: F 589 ASP cc_start: 0.9024 (m-30) cc_final: 0.8559 (m-30) REVERT: F 602 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7338 (pt) REVERT: F 621 MET cc_start: 0.8367 (tpp) cc_final: 0.7734 (tpt) REVERT: F 643 TYR cc_start: 0.9136 (m-10) cc_final: 0.8612 (m-10) outliers start: 55 outliers final: 39 residues processed: 276 average time/residue: 0.3125 time to fit residues: 128.0003 Evaluate side-chains 261 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 chunk 148 optimal weight: 0.0570 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17994 Z= 0.180 Angle : 0.766 11.906 24449 Z= 0.338 Chirality : 0.049 0.482 3514 Planarity : 0.004 0.075 2724 Dihedral : 11.633 93.187 6933 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.55 % Rotamer: Outliers : 3.69 % Allowed : 21.19 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1814 helix: 0.29 (0.24), residues: 459 sheet: -0.77 (0.25), residues: 396 loop : -1.07 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 596 HIS 0.005 0.001 HIS A 66 PHE 0.012 0.001 PHE A 468 TYR 0.020 0.001 TYR D 643 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 227 time to evaluate : 1.938 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: B 530 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7897 (mtt) REVERT: B 560 GLU cc_start: 0.8441 (tp30) cc_final: 0.8057 (tm-30) REVERT: B 584 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 589 ASP cc_start: 0.9283 (m-30) cc_final: 0.8894 (m-30) REVERT: B 605 THR cc_start: 0.9092 (p) cc_final: 0.8804 (t) REVERT: B 626 MET cc_start: 0.7544 (tpp) cc_final: 0.7050 (tpp) REVERT: B 630 GLU cc_start: 0.9514 (mt-10) cc_final: 0.8941 (mt-10) REVERT: B 634 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8847 (mp0) REVERT: B 655 LYS cc_start: 0.8787 (pptt) cc_final: 0.8580 (mmmt) REVERT: C 66 HIS cc_start: 0.8432 (m-70) cc_final: 0.8106 (m90) REVERT: C 95 MET cc_start: 0.9089 (ptt) cc_final: 0.8171 (ppp) REVERT: C 185 ASP cc_start: 0.8528 (m-30) cc_final: 0.8288 (t0) REVERT: C 373 MET cc_start: 0.7865 (mtp) cc_final: 0.7025 (ptm) REVERT: C 381 GLU cc_start: 0.8487 (tp30) cc_final: 0.8030 (tp30) REVERT: C 420 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 423 ILE cc_start: 0.9100 (mt) cc_final: 0.8876 (pt) REVERT: C 469 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7786 (mtp85) REVERT: D 557 LYS cc_start: 0.9212 (ttpp) cc_final: 0.8811 (pptt) REVERT: D 588 ARG cc_start: 0.8659 (ptt90) cc_final: 0.8158 (ptt-90) REVERT: D 591 GLN cc_start: 0.9105 (mt0) cc_final: 0.8881 (mt0) REVERT: D 626 MET cc_start: 0.7505 (tpp) cc_final: 0.7099 (tpp) REVERT: D 647 GLU cc_start: 0.9514 (pp20) cc_final: 0.9205 (pp20) REVERT: D 648 GLU cc_start: 0.9080 (pp20) cc_final: 0.8817 (pp20) REVERT: D 650 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8695 (tp-100) REVERT: E 57 ASP cc_start: 0.7775 (t0) cc_final: 0.7305 (p0) REVERT: E 95 MET cc_start: 0.9272 (ppp) cc_final: 0.8842 (ppp) REVERT: E 104 MET cc_start: 0.9114 (ttm) cc_final: 0.8771 (ttt) REVERT: E 381 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7031 (mt-10) REVERT: E 434 MET cc_start: 0.8319 (ttt) cc_final: 0.7569 (tmm) REVERT: E 477 ASP cc_start: 0.9146 (m-30) cc_final: 0.8770 (m-30) REVERT: E 492 GLU cc_start: 0.8261 (tp30) cc_final: 0.8036 (tm-30) REVERT: A 35 TRP cc_start: 0.8721 (m100) cc_final: 0.8163 (m100) REVERT: A 123 THR cc_start: 0.9269 (p) cc_final: 0.9041 (t) REVERT: A 151 ARG cc_start: 0.7583 (mpt180) cc_final: 0.6125 (mmp80) REVERT: A 255 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8997 (t) REVERT: A 381 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7279 (mt-10) REVERT: A 383 PHE cc_start: 0.8960 (m-10) cc_final: 0.8360 (m-10) REVERT: F 522 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7126 (t80) REVERT: F 579 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8446 (mmm-85) REVERT: F 589 ASP cc_start: 0.9088 (m-30) cc_final: 0.8642 (m-30) REVERT: F 603 ILE cc_start: 0.7331 (mp) cc_final: 0.7065 (mp) REVERT: F 621 MET cc_start: 0.8363 (tpp) cc_final: 0.7881 (tpt) REVERT: F 643 TYR cc_start: 0.9173 (m-10) cc_final: 0.8628 (m-10) REVERT: F 647 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8494 (mt-10) outliers start: 60 outliers final: 39 residues processed: 270 average time/residue: 0.3049 time to fit residues: 122.9569 Evaluate side-chains 253 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 208 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN B 564 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17994 Z= 0.344 Angle : 0.828 9.801 24449 Z= 0.371 Chirality : 0.049 0.514 3514 Planarity : 0.004 0.050 2724 Dihedral : 10.911 82.869 6928 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 4.30 % Allowed : 21.07 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.01 (0.19), residues: 1814 helix: 0.28 (0.24), residues: 460 sheet: -0.69 (0.26), residues: 390 loop : -1.11 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 628 HIS 0.038 0.002 HIS B 564 PHE 0.016 0.002 PHE A 468 TYR 0.017 0.002 TYR D 586 ARG 0.006 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 198 time to evaluate : 1.914 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: B 530 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8149 (mtt) REVERT: B 584 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 589 ASP cc_start: 0.9429 (m-30) cc_final: 0.9060 (m-30) REVERT: B 605 THR cc_start: 0.8965 (p) cc_final: 0.8450 (t) REVERT: B 630 GLU cc_start: 0.9486 (mt-10) cc_final: 0.8995 (mt-10) REVERT: B 634 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8922 (mp0) REVERT: C 66 HIS cc_start: 0.8448 (m-70) cc_final: 0.8162 (m90) REVERT: C 95 MET cc_start: 0.9242 (ptt) cc_final: 0.8539 (ppp) REVERT: C 113 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: C 185 ASP cc_start: 0.8483 (m-30) cc_final: 0.8199 (t0) REVERT: C 420 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8527 (mm) REVERT: D 557 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8821 (pptt) REVERT: D 575 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8888 (pp30) REVERT: D 588 ARG cc_start: 0.8725 (ptt90) cc_final: 0.8264 (ptt-90) REVERT: D 591 GLN cc_start: 0.9149 (mt0) cc_final: 0.8938 (mt0) REVERT: D 626 MET cc_start: 0.7567 (tpp) cc_final: 0.6595 (tpp) REVERT: D 647 GLU cc_start: 0.9495 (pp20) cc_final: 0.9240 (pp20) REVERT: D 648 GLU cc_start: 0.9116 (pp20) cc_final: 0.8897 (pp20) REVERT: D 650 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8507 (tp-100) REVERT: E 57 ASP cc_start: 0.7921 (t0) cc_final: 0.7387 (p0) REVERT: E 95 MET cc_start: 0.9407 (ppp) cc_final: 0.8955 (ppp) REVERT: E 104 MET cc_start: 0.9247 (ttm) cc_final: 0.8900 (ttm) REVERT: E 381 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7156 (mt-10) REVERT: E 434 MET cc_start: 0.8445 (ttt) cc_final: 0.7606 (tmm) REVERT: E 477 ASP cc_start: 0.9226 (m-30) cc_final: 0.8769 (m-30) REVERT: A 381 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8139 (tp30) REVERT: A 383 PHE cc_start: 0.8932 (m-10) cc_final: 0.8337 (m-10) REVERT: A 503 ARG cc_start: 0.7363 (tpp-160) cc_final: 0.6814 (tpp80) REVERT: F 522 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7498 (t80) REVERT: F 530 MET cc_start: 0.9393 (mmm) cc_final: 0.8903 (mmp) REVERT: F 579 ARG cc_start: 0.9149 (mtp85) cc_final: 0.8559 (mmm-85) REVERT: F 589 ASP cc_start: 0.9102 (m-30) cc_final: 0.8660 (m-30) REVERT: F 601 LYS cc_start: 0.6772 (mtmm) cc_final: 0.5783 (ptpp) REVERT: F 603 ILE cc_start: 0.8086 (mp) cc_final: 0.7619 (mp) REVERT: F 621 MET cc_start: 0.8457 (tpp) cc_final: 0.7984 (tpt) REVERT: F 643 TYR cc_start: 0.9129 (m-10) cc_final: 0.8820 (m-10) REVERT: F 647 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8599 (mt-10) outliers start: 70 outliers final: 53 residues processed: 247 average time/residue: 0.2991 time to fit residues: 110.9629 Evaluate side-chains 250 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 191 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 596 TRP Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17994 Z= 0.187 Angle : 0.757 9.641 24449 Z= 0.336 Chirality : 0.047 0.426 3514 Planarity : 0.003 0.037 2724 Dihedral : 10.247 82.824 6928 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.23 % Favored : 93.66 % Rotamer: Outliers : 3.87 % Allowed : 21.93 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1814 helix: 0.29 (0.24), residues: 459 sheet: -0.73 (0.26), residues: 389 loop : -1.10 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 596 HIS 0.004 0.001 HIS B 564 PHE 0.012 0.001 PHE A 468 TYR 0.016 0.001 TYR D 586 ARG 0.002 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 218 time to evaluate : 1.830 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: B 530 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: B 554 ASN cc_start: 0.8691 (m110) cc_final: 0.8355 (p0) REVERT: B 560 GLU cc_start: 0.8339 (tp30) cc_final: 0.7677 (tm-30) REVERT: B 584 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 589 ASP cc_start: 0.9361 (m-30) cc_final: 0.9000 (m-30) REVERT: B 605 THR cc_start: 0.9008 (p) cc_final: 0.8612 (t) REVERT: B 626 MET cc_start: 0.7576 (tpp) cc_final: 0.7035 (tpp) REVERT: B 630 GLU cc_start: 0.9463 (mt-10) cc_final: 0.8912 (mt-10) REVERT: B 634 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8885 (mp0) REVERT: B 648 GLU cc_start: 0.8930 (pp20) cc_final: 0.8344 (pp20) REVERT: C 66 HIS cc_start: 0.8379 (m-70) cc_final: 0.8091 (m90) REVERT: C 95 MET cc_start: 0.9164 (ptt) cc_final: 0.8582 (ppp) REVERT: C 113 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: C 185 ASP cc_start: 0.8447 (m-30) cc_final: 0.8140 (t0) REVERT: C 381 GLU cc_start: 0.8546 (tp30) cc_final: 0.8233 (tp30) REVERT: C 426 MET cc_start: 0.8900 (mmm) cc_final: 0.8301 (tpp) REVERT: C 469 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7928 (mtp85) REVERT: D 588 ARG cc_start: 0.8781 (ptt90) cc_final: 0.8393 (ptt-90) REVERT: D 591 GLN cc_start: 0.9190 (mt0) cc_final: 0.8983 (mt0) REVERT: D 626 MET cc_start: 0.7388 (tpp) cc_final: 0.6862 (tpp) REVERT: D 647 GLU cc_start: 0.9490 (pp20) cc_final: 0.9264 (pp20) REVERT: D 648 GLU cc_start: 0.9076 (pp20) cc_final: 0.8838 (pp20) REVERT: D 650 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8831 (tp-100) REVERT: E 57 ASP cc_start: 0.7798 (t0) cc_final: 0.7355 (p0) REVERT: E 95 MET cc_start: 0.9266 (ppp) cc_final: 0.8777 (ppp) REVERT: E 104 MET cc_start: 0.9243 (ttm) cc_final: 0.8930 (ttt) REVERT: E 381 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7052 (mt-10) REVERT: E 426 MET cc_start: 0.8012 (mmm) cc_final: 0.7388 (mmm) REVERT: E 434 MET cc_start: 0.8348 (ttt) cc_final: 0.7564 (tmm) REVERT: E 477 ASP cc_start: 0.9157 (m-30) cc_final: 0.8721 (m-30) REVERT: A 35 TRP cc_start: 0.8930 (m100) cc_final: 0.8362 (m100) REVERT: A 151 ARG cc_start: 0.7524 (mpt180) cc_final: 0.7293 (mmt180) REVERT: A 381 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7245 (mt-10) REVERT: A 383 PHE cc_start: 0.8902 (m-10) cc_final: 0.8400 (m-10) REVERT: A 503 ARG cc_start: 0.7346 (tpp-160) cc_final: 0.6737 (tpp80) REVERT: F 522 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6915 (t80) REVERT: F 530 MET cc_start: 0.9424 (mmm) cc_final: 0.9111 (mmp) REVERT: F 579 ARG cc_start: 0.9128 (mtp85) cc_final: 0.8622 (mtm-85) REVERT: F 589 ASP cc_start: 0.9047 (m-30) cc_final: 0.8569 (m-30) REVERT: F 601 LYS cc_start: 0.6764 (mtmm) cc_final: 0.5764 (ptpp) REVERT: F 603 ILE cc_start: 0.7965 (mp) cc_final: 0.7500 (mp) REVERT: F 621 MET cc_start: 0.8470 (tpp) cc_final: 0.7930 (tpp) REVERT: F 633 LYS cc_start: 0.9482 (mmmm) cc_final: 0.8941 (mmmm) REVERT: F 643 TYR cc_start: 0.9190 (m-10) cc_final: 0.8849 (m-10) REVERT: F 647 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8651 (mt-10) outliers start: 63 outliers final: 48 residues processed: 262 average time/residue: 0.3110 time to fit residues: 122.1931 Evaluate side-chains 264 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 0.0170 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 HIS C 105 HIS ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17994 Z= 0.213 Angle : 0.753 10.105 24449 Z= 0.338 Chirality : 0.046 0.417 3514 Planarity : 0.003 0.036 2724 Dihedral : 9.582 84.963 6928 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 3.56 % Allowed : 22.30 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -1.04 (0.19), residues: 1814 helix: 0.37 (0.24), residues: 454 sheet: -0.75 (0.25), residues: 418 loop : -1.15 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 596 HIS 0.002 0.001 HIS C 249 PHE 0.012 0.001 PHE A 468 TYR 0.030 0.001 TYR B 586 ARG 0.003 0.000 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 1.956 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: B 530 MET cc_start: 0.8600 (mtm) cc_final: 0.8228 (mtt) REVERT: B 589 ASP cc_start: 0.9372 (m-30) cc_final: 0.8993 (m-30) REVERT: B 605 THR cc_start: 0.9031 (p) cc_final: 0.8707 (t) REVERT: B 630 GLU cc_start: 0.9429 (mt-10) cc_final: 0.9068 (mt-10) REVERT: C 66 HIS cc_start: 0.8417 (m-70) cc_final: 0.8130 (m90) REVERT: C 95 MET cc_start: 0.9232 (ptt) cc_final: 0.8510 (ppp) REVERT: C 104 MET cc_start: 0.9206 (tmm) cc_final: 0.8996 (ppp) REVERT: C 113 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: C 381 GLU cc_start: 0.8658 (tp30) cc_final: 0.8256 (tp30) REVERT: C 420 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8361 (mm) REVERT: C 426 MET cc_start: 0.8869 (mmm) cc_final: 0.8109 (tpp) REVERT: C 469 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8003 (mtp85) REVERT: D 588 ARG cc_start: 0.8800 (ptt90) cc_final: 0.8308 (ptt-90) REVERT: D 591 GLN cc_start: 0.9190 (mt0) cc_final: 0.8989 (mt0) REVERT: D 626 MET cc_start: 0.6971 (tpp) cc_final: 0.6532 (tpp) REVERT: D 647 GLU cc_start: 0.9496 (pp20) cc_final: 0.9293 (pp20) REVERT: D 648 GLU cc_start: 0.9152 (pp20) cc_final: 0.8870 (pp20) REVERT: D 650 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8792 (tp-100) REVERT: E 57 ASP cc_start: 0.7687 (t0) cc_final: 0.7272 (p0) REVERT: E 95 MET cc_start: 0.9257 (ppp) cc_final: 0.8790 (ppp) REVERT: E 104 MET cc_start: 0.9236 (ttm) cc_final: 0.8925 (ttm) REVERT: E 381 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7044 (mt-10) REVERT: E 426 MET cc_start: 0.8030 (mmm) cc_final: 0.7404 (mmm) REVERT: E 434 MET cc_start: 0.8355 (ttt) cc_final: 0.7564 (tmm) REVERT: E 477 ASP cc_start: 0.9168 (m-30) cc_final: 0.8732 (m-30) REVERT: A 35 TRP cc_start: 0.8944 (m100) cc_final: 0.8389 (m100) REVERT: A 151 ARG cc_start: 0.7531 (mpt180) cc_final: 0.7301 (mmt180) REVERT: A 381 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 383 PHE cc_start: 0.8904 (m-10) cc_final: 0.8231 (m-10) REVERT: F 522 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.6989 (t80) REVERT: F 557 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7892 (tmmt) REVERT: F 589 ASP cc_start: 0.9032 (m-30) cc_final: 0.8587 (m-30) REVERT: F 601 LYS cc_start: 0.6872 (mtmm) cc_final: 0.5862 (ptpp) REVERT: F 603 ILE cc_start: 0.8001 (mp) cc_final: 0.7529 (mp) REVERT: F 621 MET cc_start: 0.8469 (tpp) cc_final: 0.7820 (tpt) REVERT: F 633 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9029 (mmmm) REVERT: F 643 TYR cc_start: 0.9213 (m-10) cc_final: 0.8960 (m-10) outliers start: 58 outliers final: 49 residues processed: 250 average time/residue: 0.3019 time to fit residues: 113.8613 Evaluate side-chains 256 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 7.9990 chunk 166 optimal weight: 0.0770 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395AASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17994 Z= 0.189 Angle : 0.731 9.914 24449 Z= 0.329 Chirality : 0.045 0.380 3514 Planarity : 0.003 0.036 2724 Dihedral : 9.096 87.359 6925 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 3.32 % Allowed : 22.67 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1814 helix: 0.34 (0.24), residues: 455 sheet: -0.63 (0.26), residues: 388 loop : -1.18 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 628 HIS 0.002 0.001 HIS A 105 PHE 0.017 0.001 PHE A 468 TYR 0.019 0.001 TYR D 586 ARG 0.003 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 213 time to evaluate : 1.953 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: B 530 MET cc_start: 0.8557 (mtm) cc_final: 0.8184 (mtt) REVERT: B 560 GLU cc_start: 0.8398 (tp30) cc_final: 0.7678 (tm-30) REVERT: B 568 LEU cc_start: 0.8720 (tp) cc_final: 0.8503 (pt) REVERT: B 584 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 589 ASP cc_start: 0.9369 (m-30) cc_final: 0.8947 (m-30) REVERT: B 605 THR cc_start: 0.8996 (p) cc_final: 0.8731 (t) REVERT: B 630 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8907 (mt-10) REVERT: B 634 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8870 (mp0) REVERT: B 647 GLU cc_start: 0.8694 (pt0) cc_final: 0.8237 (pp20) REVERT: B 659 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7861 (pt0) REVERT: C 66 HIS cc_start: 0.8411 (m-70) cc_final: 0.8124 (m90) REVERT: C 95 MET cc_start: 0.9215 (ptt) cc_final: 0.8527 (ppp) REVERT: C 113 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: C 381 GLU cc_start: 0.8584 (tp30) cc_final: 0.8179 (tp30) REVERT: C 420 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8329 (mm) REVERT: C 426 MET cc_start: 0.8824 (mmm) cc_final: 0.7986 (tpp) REVERT: C 469 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8000 (mtp85) REVERT: D 588 ARG cc_start: 0.8799 (ptt90) cc_final: 0.8168 (ptt180) REVERT: D 626 MET cc_start: 0.6872 (tpp) cc_final: 0.6457 (tpp) REVERT: D 648 GLU cc_start: 0.9098 (pp20) cc_final: 0.8804 (pp20) REVERT: D 650 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8775 (tp-100) REVERT: E 57 ASP cc_start: 0.7638 (t0) cc_final: 0.7246 (p0) REVERT: E 95 MET cc_start: 0.9239 (ppp) cc_final: 0.8749 (ppp) REVERT: E 104 MET cc_start: 0.9254 (ttm) cc_final: 0.8926 (ttt) REVERT: E 381 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7017 (mt-10) REVERT: E 434 MET cc_start: 0.8318 (ttt) cc_final: 0.7548 (tmm) REVERT: E 477 ASP cc_start: 0.9149 (m-30) cc_final: 0.8722 (m-30) REVERT: E 492 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8527 (mm-30) REVERT: A 35 TRP cc_start: 0.8931 (m100) cc_final: 0.8370 (m100) REVERT: A 40 TYR cc_start: 0.8471 (t80) cc_final: 0.8195 (t80) REVERT: A 381 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7352 (mt-10) REVERT: A 383 PHE cc_start: 0.8764 (m-10) cc_final: 0.8245 (m-10) REVERT: F 522 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.6931 (t80) REVERT: F 530 MET cc_start: 0.9104 (tpp) cc_final: 0.8575 (mmp) REVERT: F 557 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7731 (tptp) REVERT: F 589 ASP cc_start: 0.9067 (m-30) cc_final: 0.8642 (m-30) REVERT: F 601 LYS cc_start: 0.6937 (mtmm) cc_final: 0.5907 (ptpp) REVERT: F 603 ILE cc_start: 0.8063 (mp) cc_final: 0.7493 (mp) REVERT: F 621 MET cc_start: 0.8545 (tpp) cc_final: 0.8082 (tpt) REVERT: F 633 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9061 (mmmm) REVERT: F 643 TYR cc_start: 0.9255 (m-10) cc_final: 0.8970 (m-10) outliers start: 54 outliers final: 46 residues processed: 252 average time/residue: 0.3020 time to fit residues: 114.2969 Evaluate side-chains 259 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17994 Z= 0.257 Angle : 0.753 13.023 24449 Z= 0.341 Chirality : 0.045 0.395 3514 Planarity : 0.004 0.041 2724 Dihedral : 8.814 88.592 6924 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.17 % Favored : 92.72 % Rotamer: Outliers : 3.13 % Allowed : 22.79 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1814 helix: 0.56 (0.25), residues: 441 sheet: -0.45 (0.27), residues: 356 loop : -1.21 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 628 HIS 0.003 0.001 HIS C 66 PHE 0.019 0.001 PHE A 468 TYR 0.024 0.001 TYR B 586 ARG 0.004 0.001 ARG B 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 1.913 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: B 530 MET cc_start: 0.8721 (mtm) cc_final: 0.8308 (mtt) REVERT: B 568 LEU cc_start: 0.8894 (tp) cc_final: 0.8640 (pt) REVERT: B 584 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8453 (pt0) REVERT: B 589 ASP cc_start: 0.9394 (m-30) cc_final: 0.9012 (m-30) REVERT: B 605 THR cc_start: 0.8912 (p) cc_final: 0.8542 (t) REVERT: B 630 GLU cc_start: 0.9432 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 634 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8901 (mp0) REVERT: B 648 GLU cc_start: 0.8915 (pp20) cc_final: 0.8656 (pp20) REVERT: C 66 HIS cc_start: 0.8445 (m-70) cc_final: 0.8187 (m90) REVERT: C 95 MET cc_start: 0.9258 (ptt) cc_final: 0.8585 (ppp) REVERT: C 113 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8601 (m-30) REVERT: C 373 MET cc_start: 0.7916 (mtp) cc_final: 0.7373 (ptm) REVERT: C 381 GLU cc_start: 0.8649 (tp30) cc_final: 0.8242 (tp30) REVERT: C 420 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8444 (mm) REVERT: C 469 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8003 (mtp85) REVERT: D 542 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.5070 (mmt-90) REVERT: D 588 ARG cc_start: 0.8742 (ptt90) cc_final: 0.8199 (ptt180) REVERT: D 626 MET cc_start: 0.6957 (tpp) cc_final: 0.6437 (tpp) REVERT: D 648 GLU cc_start: 0.9125 (pp20) cc_final: 0.8890 (pp20) REVERT: D 650 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8809 (tp-100) REVERT: E 57 ASP cc_start: 0.7717 (t0) cc_final: 0.7294 (p0) REVERT: E 95 MET cc_start: 0.9314 (ppp) cc_final: 0.8885 (ppp) REVERT: E 104 MET cc_start: 0.9265 (ttm) cc_final: 0.9063 (ttm) REVERT: E 381 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7013 (mt-10) REVERT: E 426 MET cc_start: 0.8049 (mmm) cc_final: 0.7438 (mmm) REVERT: E 434 MET cc_start: 0.8398 (ttt) cc_final: 0.7590 (tmm) REVERT: E 477 ASP cc_start: 0.9184 (m-30) cc_final: 0.8751 (m-30) REVERT: E 492 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8551 (mm-30) REVERT: A 381 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7253 (mt-10) REVERT: A 383 PHE cc_start: 0.8840 (m-10) cc_final: 0.8289 (m-10) REVERT: F 522 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.6930 (t80) REVERT: F 530 MET cc_start: 0.9143 (tpp) cc_final: 0.8429 (mmm) REVERT: F 557 LYS cc_start: 0.8223 (tmtt) cc_final: 0.7915 (tmtt) REVERT: F 589 ASP cc_start: 0.9058 (m-30) cc_final: 0.8611 (m-30) REVERT: F 601 LYS cc_start: 0.7126 (mtmm) cc_final: 0.6068 (ptpp) REVERT: F 603 ILE cc_start: 0.8019 (mp) cc_final: 0.7622 (mp) REVERT: F 621 MET cc_start: 0.8619 (tpp) cc_final: 0.8018 (tpt) REVERT: F 633 LYS cc_start: 0.9549 (mmmm) cc_final: 0.9114 (mmmm) REVERT: F 643 TYR cc_start: 0.9306 (m-10) cc_final: 0.8994 (m-10) outliers start: 51 outliers final: 44 residues processed: 240 average time/residue: 0.3257 time to fit residues: 118.3950 Evaluate side-chains 250 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 202 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 0.0050 chunk 26 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.082559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062149 restraints weight = 62237.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064242 restraints weight = 34288.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065577 restraints weight = 24477.010| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17994 Z= 0.226 Angle : 0.738 11.205 24449 Z= 0.337 Chirality : 0.045 0.371 3514 Planarity : 0.003 0.036 2724 Dihedral : 8.683 88.341 6924 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 3.13 % Allowed : 22.48 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1814 helix: 0.51 (0.25), residues: 441 sheet: -0.51 (0.27), residues: 363 loop : -1.20 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 596 HIS 0.002 0.001 HIS A 105 PHE 0.017 0.001 PHE A 468 TYR 0.030 0.001 TYR B 586 ARG 0.003 0.000 ARG B 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.85 seconds wall clock time: 65 minutes 24.95 seconds (3924.95 seconds total)