Starting phenix.real_space_refine on Wed Mar 20 17:51:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fad_28953/03_2024/8fad_28953_neut_updated.pdb" } resolution = 4.0 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 Anisotropic ADP refinement not supported. Converting 11943 atoms to isotropic. 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 10074 2.51 5 N 2626 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 632": "OE1" <-> "OE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "F GLU 647": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16210 Number of models: 1 Model: "" Number of chains: 60 Chain: "B" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "C" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3675 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "D" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "E" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3675 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3675 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {'83G': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {'83G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {'83G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 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 Time building chain proxies: 8.28, per 1000 atoms: 0.51 Number of scatterers: 16210 At special positions: 0 Unit cell: (141.11, 139.74, 124.67, 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 3414 8.00 N 2626 7.00 C 10074 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.03 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=2.03 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=2.02 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 M 4 " - " MAN M 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA c 3 " - " MAN c 4 " " BMA h 3 " - " MAN h 4 " " BMA r 3 " - " MAN r 6 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA R 3 " - " MAN R 4 " " BMA c 3 " - " MAN c 5 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN A 448 " " NAG 1 1 " - " ASN F 611 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 188 " " NAG A 604 " - " ASN A 241 " " NAG A 605 " - " ASN A 401 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 188 " " NAG C 604 " - " ASN C 241 " " NAG C 605 " - " ASN C 356 " " NAG C 606 " - " ASN C 401 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 625 " " NAG D 703 " - " ASN D 637 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 188 " " NAG E 604 " - " ASN E 241 " " NAG E 605 " - " ASN E 401 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 625 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN B 611 " " NAG H 1 " - " ASN C 88 " " NAG I 1 " - " ASN C 130 " " NAG J 1 " - " ASN C 156 " " NAG K 1 " - " ASN C 197 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 276 " " NAG O 1 " - " ASN C 295 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 339 " " NAG S 1 " - " ASN C 362 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN C 392 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN D 611 " " NAG X 1 " - " ASN E 88 " " NAG Y 1 " - " ASN E 130 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 301 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 339 " " NAG i 1 " - " ASN E 362 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 392 " " NAG l 1 " - " ASN E 448 " " NAG m 1 " - " ASN A 88 " " NAG n 1 " - " ASN A 130 " " NAG o 1 " - " ASN A 156 " " NAG p 1 " - " ASN A 197 " " NAG q 1 " - " ASN A 234 " " NAG r 1 " - " ASN A 262 " " NAG s 1 " - " ASN A 276 " " NAG t 1 " - " ASN A 295 " " NAG u 1 " - " ASN A 301 " " NAG v 1 " - " ASN A 332 " " NAG w 1 " - " ASN A 339 " " NAG x 1 " - " ASN A 362 " " NAG y 1 " - " ASN A 386 " " NAG z 1 " - " ASN A 392 " Time building additional restraints: 8.41 Conformation dependent library (CDL) restraints added in 2.7 seconds 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 27 sheets defined 24.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 537 through 563 removed outlier: 4.289A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.879A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 656 Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.869A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 63' Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 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 477 through 483 removed outlier: 4.043A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 534 Processing helix chain 'D' and resid 539 through 563 removed outlier: 3.537A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 619 through 625 Processing helix chain 'D' and resid 628 through 634 removed outlier: 3.980A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 656 removed outlier: 4.231A pdb=" N GLY D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.803A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) 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 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 475 through 482 removed outlier: 4.305A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 63 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 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'F' and resid 524 through 527 removed outlier: 3.957A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 530 through 535 removed outlier: 3.604A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 571 through 595 removed outlier: 3.588A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 623 No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 628 through 634 removed outlier: 4.032A pdb=" N ARG F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 656 Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.217A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 92 through 94 Processing sheet with id= D, first strand: chain 'C' and resid 157 through 162 Processing sheet with id= E, first strand: chain 'C' and resid 271 through 273 removed outlier: 4.249A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 330 through 332 removed outlier: 3.998A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 304 through 308 Processing sheet with id= H, first strand: chain 'C' and resid 374 through 378 Processing sheet with id= I, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= J, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.803A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) 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 157 through 162 Processing sheet with id= M, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.724A pdb=" N ARG E 192 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.733A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.376A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 292 through 298 removed outlier: 4.023A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 304 through 308 Processing sheet with id= R, first strand: chain 'E' and resid 329 through 334 removed outlier: 3.596A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= T, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.591A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 92 through 94 Processing sheet with id= V, first strand: chain 'A' and resid 157 through 161 Processing sheet with id= W, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.666A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.205A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 443 through 449 removed outlier: 3.989A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 331 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 304 through 308 Processing sheet with id= AA, first strand: chain 'A' and resid 374 through 378 448 hydrogen bonds defined for protein. 1266 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: 4.71 Time building geometry restraints manager: 8.44 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: 3874 1.33 - 1.46: 4337 1.46 - 1.59: 8165 1.59 - 1.72: 1 1.72 - 1.85: 132 Bond restraints: 16509 Sorted by residual: 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 4.73e+01 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 4.73e+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 4.13e+01 bond pdb=" C14 83G A 601 " pdb=" N16 83G A 601 " ideal model delta sigma weight residual 1.473 1.347 0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 16504 not shown) Histogram of bond angle deviations from ideal: 95.06 - 103.56: 169 103.56 - 112.05: 8713 112.05 - 120.54: 7896 120.54 - 129.04: 5512 129.04 - 137.53: 146 Bond angle restraints: 22436 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 88.71 125.06 -36.35 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 88.71 124.61 -35.90 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 161.60 128.71 32.89 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 161.60 128.80 32.80 3.00e+00 1.11e-01 1.20e+02 ... (remaining 22431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.54: 10761 22.54 - 45.09: 668 45.09 - 67.63: 169 67.63 - 90.18: 77 90.18 - 112.72: 42 Dihedral angle restraints: 11717 sinusoidal: 6525 harmonic: 5192 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 166.92 -73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 149.50 -56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CA CYS C 119 " pdb=" C CYS C 119 " pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta harmonic sigma weight residual 180.00 -150.23 -29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 11714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 2879 0.297 - 0.594: 40 0.594 - 0.891: 12 0.891 - 1.188: 4 1.188 - 1.485: 5 Chirality restraints: 2940 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-02 2.50e+03 5.51e+03 chirality pdb=" C1 NAG w 2 " pdb=" O4 NAG w 1 " pdb=" C2 NAG w 2 " pdb=" O5 NAG w 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-02 2.50e+03 5.49e+03 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.53e+03 ... (remaining 2937 not shown) Planarity restraints: 2738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " -0.356 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG F 703 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " -0.111 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " 0.547 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 1 2 " -0.327 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG 1 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG 1 2 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG 1 2 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG 1 2 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 1 " 0.331 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG l 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG l 1 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG l 1 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG l 1 " 0.085 2.00e-02 2.50e+03 ... (remaining 2735 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 12 2.29 - 2.94: 7734 2.94 - 3.59: 22704 3.59 - 4.25: 37755 4.25 - 4.90: 59068 Nonbonded interactions: 127273 Sorted by model distance: nonbonded pdb=" NH2 ARG E 166 " pdb=" CA PRO A 124 " model vdw 1.632 3.550 nonbonded pdb=" OE1 GLU A 211 " pdb=" O6 MAN r 6 " model vdw 2.027 2.440 nonbonded pdb=" NH2 ARG E 166 " pdb=" CB PRO A 124 " model vdw 2.051 3.520 nonbonded pdb=" OD1 ASN C 461 " pdb=" OG1 THR C 465 " model vdw 2.135 2.440 nonbonded pdb=" OD1 ASN A 461 " pdb=" OG1 THR A 465 " model vdw 2.136 2.440 ... (remaining 127268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 33 through 503 or resid 601 through 605)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 520 through 547 or resid 563 through 657 or resid 701 thro \ ugh 703)) selection = (chain 'D' and (resid 520 through 547 or resid 563 through 657 or resid 701 thro \ ugh 703)) selection = chain 'F' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'g' selection = chain 'j' selection = chain 'w' } ncs_group { reference = chain 'M' selection = chain 'r' } ncs_group { reference = chain 'c' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 1.970 Check model and map are aligned: 0.270 Set scattering table: 0.130 Process input model: 44.150 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 : 0.011 0.138 16509 Z= 0.711 Angle : 1.579 36.679 22436 Z= 0.986 Chirality : 0.130 1.485 2940 Planarity : 0.029 0.307 2668 Dihedral : 17.043 112.719 8267 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.62 % Favored : 89.48 % Rotamer: Outliers : 3.64 % Allowed : 7.73 % Favored : 88.63 % Cbeta Deviations : 0.71 % 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: -2.33 (0.19), residues: 1777 helix: 0.05 (0.27), residues: 416 sheet: -1.43 (0.24), residues: 390 loop : -2.39 (0.17), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 400 HIS 0.009 0.002 HIS E 374 PHE 0.017 0.001 PHE A 468 TYR 0.013 0.002 TYR F 586 ARG 0.016 0.001 ARG E 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 459 time to evaluate : 1.742 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: B 530 MET cc_start: 0.8912 (ttm) cc_final: 0.8347 (ttp) REVERT: B 543 LEU cc_start: 0.9514 (mt) cc_final: 0.9286 (pp) REVERT: B 629 MET cc_start: 0.8105 (mmm) cc_final: 0.7709 (mmm) REVERT: B 638 TYR cc_start: 0.7859 (m-80) cc_final: 0.7583 (m-80) REVERT: B 649 SER cc_start: 0.9434 (p) cc_final: 0.9118 (p) REVERT: B 654 GLU cc_start: 0.8105 (tt0) cc_final: 0.7739 (tt0) REVERT: B 655 LYS cc_start: 0.7006 (mttt) cc_final: 0.6589 (mmtm) REVERT: C 34 LEU cc_start: 0.8712 (mt) cc_final: 0.8322 (mt) REVERT: C 68 VAL cc_start: 0.5921 (OUTLIER) cc_final: 0.4735 (p) REVERT: C 71 THR cc_start: 0.7841 (m) cc_final: 0.7353 (t) REVERT: C 80 ASN cc_start: 0.7551 (t0) cc_final: 0.7105 (t0) REVERT: C 95 MET cc_start: 0.8191 (ppp) cc_final: 0.7575 (ppp) REVERT: C 120 VAL cc_start: 0.8999 (t) cc_final: 0.8357 (t) REVERT: C 190 SER cc_start: 0.8535 (m) cc_final: 0.8308 (p) REVERT: C 244 THR cc_start: 0.9588 (m) cc_final: 0.9194 (p) REVERT: C 256 SER cc_start: 0.9024 (p) cc_final: 0.8728 (p) REVERT: C 475 MET cc_start: 0.8878 (tpp) cc_final: 0.8299 (mmp) REVERT: D 629 MET cc_start: 0.7929 (mmm) cc_final: 0.7693 (mmm) REVERT: D 651 ASN cc_start: 0.8779 (t0) cc_final: 0.8380 (t0) REVERT: E 37 THR cc_start: 0.8729 (m) cc_final: 0.8454 (p) REVERT: E 39 TYR cc_start: 0.7470 (m-80) cc_final: 0.7134 (m-10) REVERT: E 71 THR cc_start: 0.8695 (m) cc_final: 0.8467 (p) REVERT: E 86 LEU cc_start: 0.8932 (mp) cc_final: 0.8665 (tp) REVERT: E 98 ASN cc_start: 0.8341 (t0) cc_final: 0.8050 (t0) REVERT: E 179 LEU cc_start: 0.9120 (mt) cc_final: 0.8886 (tp) REVERT: E 330 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (p-80) REVERT: E 435 TYR cc_start: 0.7806 (t80) cc_final: 0.6664 (t80) REVERT: A 66 HIS cc_start: 0.8577 (m90) cc_final: 0.8270 (m90) REVERT: A 80 ASN cc_start: 0.7875 (t0) cc_final: 0.7518 (p0) REVERT: A 95 MET cc_start: 0.9113 (ppp) cc_final: 0.8878 (ppp) REVERT: A 133 ASP cc_start: 0.6984 (m-30) cc_final: 0.6434 (p0) REVERT: A 193 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 195 ASN cc_start: 0.8946 (m-40) cc_final: 0.8064 (t0) REVERT: A 245 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8755 (m) REVERT: A 302 ASN cc_start: 0.8666 (m-40) cc_final: 0.8347 (m110) REVERT: F 530 MET cc_start: 0.7928 (mtm) cc_final: 0.7383 (mtt) REVERT: F 618 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8296 (p) REVERT: F 621 MET cc_start: 0.9044 (mmt) cc_final: 0.8839 (mmm) REVERT: F 632 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8282 (tm-30) REVERT: F 633 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8270 (mmm-85) REVERT: F 648 GLU cc_start: 0.9443 (pp20) cc_final: 0.9153 (pp20) REVERT: F 652 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8780 (tm-30) outliers start: 58 outliers final: 8 residues processed: 494 average time/residue: 0.2808 time to fit residues: 201.5775 Evaluate side-chains 246 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 233 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 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 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 139 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 656 ASN E 67 ASN E 195 ASN E 330 HIS E 428 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 442 GLN F 590 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16509 Z= 0.256 Angle : 0.878 11.478 22436 Z= 0.407 Chirality : 0.053 0.446 2940 Planarity : 0.004 0.058 2668 Dihedral : 13.699 82.189 4894 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.37 % Favored : 92.46 % Rotamer: Outliers : 3.58 % Allowed : 14.82 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.93 (0.19), residues: 1777 helix: 0.37 (0.25), residues: 424 sheet: -1.12 (0.23), residues: 468 loop : -2.23 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 571 HIS 0.010 0.001 HIS A 72 PHE 0.017 0.001 PHE A 382 TYR 0.011 0.001 TYR C 191 ARG 0.008 0.001 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 243 time to evaluate : 1.798 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: 0.9034 (ttm) cc_final: 0.8305 (ttm) REVERT: B 554 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8165 (t0) REVERT: B 588 ARG cc_start: 0.9105 (ttm170) cc_final: 0.8781 (ttm110) REVERT: B 601 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8228 (mmmt) REVERT: B 628 TRP cc_start: 0.8842 (m100) cc_final: 0.8301 (m100) REVERT: B 629 MET cc_start: 0.7972 (mmm) cc_final: 0.7736 (mmm) REVERT: B 638 TYR cc_start: 0.8184 (m-80) cc_final: 0.7981 (m-10) REVERT: C 80 ASN cc_start: 0.7515 (t0) cc_final: 0.7037 (t0) REVERT: C 244 THR cc_start: 0.9488 (m) cc_final: 0.9263 (p) REVERT: D 638 TYR cc_start: 0.8416 (m-80) cc_final: 0.8211 (m-10) REVERT: E 37 THR cc_start: 0.8698 (m) cc_final: 0.8270 (p) REVERT: E 71 THR cc_start: 0.8713 (m) cc_final: 0.8424 (t) REVERT: E 180 ASP cc_start: 0.7235 (m-30) cc_final: 0.7011 (m-30) REVERT: E 373 MET cc_start: 0.8431 (ptt) cc_final: 0.7815 (ppp) REVERT: E 435 TYR cc_start: 0.8054 (t80) cc_final: 0.7452 (t80) REVERT: A 80 ASN cc_start: 0.7968 (t0) cc_final: 0.7596 (p0) REVERT: A 95 MET cc_start: 0.9206 (ppp) cc_final: 0.8950 (ppp) REVERT: A 104 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8737 (tmm) REVERT: A 195 ASN cc_start: 0.8875 (m-40) cc_final: 0.7995 (t0) REVERT: A 197 ASN cc_start: 0.6280 (OUTLIER) cc_final: 0.5762 (t0) REVERT: A 198 THR cc_start: 0.8952 (p) cc_final: 0.8159 (p) REVERT: A 373 MET cc_start: 0.8020 (ppp) cc_final: 0.7519 (ppp) REVERT: F 530 MET cc_start: 0.7962 (mtm) cc_final: 0.7651 (mtm) REVERT: F 543 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7532 (tm) REVERT: F 566 LEU cc_start: 0.7171 (mt) cc_final: 0.6695 (mt) REVERT: F 575 GLN cc_start: 0.8713 (pt0) cc_final: 0.8216 (pp30) REVERT: F 584 GLU cc_start: 0.8608 (mp0) cc_final: 0.8325 (mp0) REVERT: F 618 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8882 (m) REVERT: F 622 ILE cc_start: 0.9554 (pt) cc_final: 0.9250 (mm) REVERT: F 629 MET cc_start: 0.8970 (mmm) cc_final: 0.8605 (mmm) REVERT: F 632 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8456 (tm-30) REVERT: F 633 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: F 648 GLU cc_start: 0.9447 (pp20) cc_final: 0.9169 (pp20) REVERT: F 652 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8797 (tm-30) outliers start: 57 outliers final: 27 residues processed: 282 average time/residue: 0.2579 time to fit residues: 110.2212 Evaluate side-chains 222 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 400 TRP Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 553 ASN B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16509 Z= 0.253 Angle : 0.780 11.687 22436 Z= 0.366 Chirality : 0.050 0.336 2940 Planarity : 0.004 0.045 2668 Dihedral : 11.105 83.543 4882 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.77 % Favored : 92.12 % Rotamer: Outliers : 4.40 % Allowed : 17.46 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.72 (0.19), residues: 1777 helix: 0.67 (0.25), residues: 408 sheet: -0.99 (0.23), residues: 462 loop : -2.13 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 69 HIS 0.009 0.001 HIS A 72 PHE 0.013 0.001 PHE A 382 TYR 0.010 0.001 TYR C 384 ARG 0.003 0.001 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 204 time to evaluate : 1.752 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: 0.9184 (ttm) cc_final: 0.8553 (ttm) REVERT: B 543 LEU cc_start: 0.9602 (mt) cc_final: 0.9192 (pp) REVERT: B 588 ARG cc_start: 0.9062 (ttm170) cc_final: 0.8736 (ttm110) REVERT: B 629 MET cc_start: 0.8010 (mmm) cc_final: 0.7755 (mmm) REVERT: C 80 ASN cc_start: 0.7563 (t0) cc_final: 0.7102 (t0) REVERT: C 104 MET cc_start: 0.9516 (tmm) cc_final: 0.9246 (tmm) REVERT: C 244 THR cc_start: 0.9433 (m) cc_final: 0.9172 (p) REVERT: C 395 TRP cc_start: 0.7390 (m100) cc_final: 0.7123 (m100) REVERT: D 542 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.8178 (ptp-110) REVERT: D 629 MET cc_start: 0.7554 (mmm) cc_final: 0.7333 (mmm) REVERT: D 632 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 37 THR cc_start: 0.8867 (m) cc_final: 0.8133 (p) REVERT: E 373 MET cc_start: 0.8667 (ptt) cc_final: 0.8085 (ptt) REVERT: A 40 TYR cc_start: 0.8916 (t80) cc_final: 0.8607 (t80) REVERT: A 80 ASN cc_start: 0.8045 (t0) cc_final: 0.7697 (p0) REVERT: A 104 MET cc_start: 0.8983 (tmm) cc_final: 0.8622 (tmm) REVERT: A 195 ASN cc_start: 0.8624 (m-40) cc_final: 0.7707 (t0) REVERT: A 198 THR cc_start: 0.8960 (p) cc_final: 0.8087 (p) REVERT: A 240 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8396 (ttpp) REVERT: A 373 MET cc_start: 0.7949 (ppp) cc_final: 0.7451 (ppp) REVERT: A 394 THR cc_start: 0.8954 (p) cc_final: 0.8685 (t) REVERT: A 475 MET cc_start: 0.8972 (tpp) cc_final: 0.8491 (tpp) REVERT: F 530 MET cc_start: 0.8462 (mtm) cc_final: 0.8075 (mtm) REVERT: F 566 LEU cc_start: 0.6970 (mt) cc_final: 0.6530 (mt) REVERT: F 575 GLN cc_start: 0.8859 (pt0) cc_final: 0.8324 (pp30) REVERT: F 577 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8619 (mm-40) REVERT: F 629 MET cc_start: 0.8868 (mmm) cc_final: 0.8655 (mmm) REVERT: F 633 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8743 (mtp85) REVERT: F 647 GLU cc_start: 0.8953 (tp30) cc_final: 0.8703 (tp30) outliers start: 70 outliers final: 39 residues processed: 252 average time/residue: 0.2552 time to fit residues: 98.2826 Evaluate side-chains 221 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 633 ARG Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 636 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN D 575 GLN D 577 GLN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16509 Z= 0.314 Angle : 0.788 10.851 22436 Z= 0.373 Chirality : 0.050 0.340 2940 Planarity : 0.004 0.044 2668 Dihedral : 9.892 83.640 4880 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.33 % Favored : 91.56 % Rotamer: Outliers : 5.15 % Allowed : 19.28 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.67 (0.19), residues: 1777 helix: 0.87 (0.25), residues: 407 sheet: -1.07 (0.23), residues: 468 loop : -2.10 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 596 HIS 0.008 0.001 HIS A 72 PHE 0.014 0.002 PHE E 382 TYR 0.017 0.002 TYR D 638 ARG 0.007 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 191 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9274 (ttm) cc_final: 0.8714 (ttm) REVERT: B 638 TYR cc_start: 0.8804 (m-10) cc_final: 0.8565 (m-10) REVERT: B 643 TYR cc_start: 0.9298 (m-80) cc_final: 0.8896 (m-80) REVERT: C 80 ASN cc_start: 0.7618 (t0) cc_final: 0.7092 (t0) REVERT: C 107 ASP cc_start: 0.9672 (t70) cc_final: 0.9366 (t0) REVERT: C 211 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 244 THR cc_start: 0.9404 (m) cc_final: 0.9200 (p) REVERT: C 426 MET cc_start: 0.8606 (mmm) cc_final: 0.8291 (mmm) REVERT: D 542 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.8029 (ptp-110) REVERT: D 575 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8704 (pp30) REVERT: D 591 GLN cc_start: 0.9298 (tt0) cc_final: 0.8849 (tm-30) REVERT: D 601 LYS cc_start: 0.8030 (tptp) cc_final: 0.7644 (tptp) REVERT: D 603 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8281 (pt) REVERT: D 632 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8494 (mm-30) REVERT: E 95 MET cc_start: 0.9341 (ptt) cc_final: 0.9048 (ptt) REVERT: E 373 MET cc_start: 0.8792 (ptt) cc_final: 0.8257 (ptt) REVERT: A 240 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: A 373 MET cc_start: 0.7937 (ppp) cc_final: 0.7449 (ppp) REVERT: A 394 THR cc_start: 0.9008 (p) cc_final: 0.8789 (t) REVERT: F 530 MET cc_start: 0.8504 (mtm) cc_final: 0.8107 (mtm) REVERT: F 566 LEU cc_start: 0.7286 (mt) cc_final: 0.6927 (mt) REVERT: F 575 GLN cc_start: 0.8888 (pt0) cc_final: 0.8377 (pp30) REVERT: F 577 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8662 (mm-40) REVERT: F 584 GLU cc_start: 0.8655 (mp0) cc_final: 0.8443 (mp0) REVERT: F 633 ARG cc_start: 0.9099 (mmm-85) cc_final: 0.8728 (mmm-85) REVERT: F 648 GLU cc_start: 0.9427 (pp20) cc_final: 0.9178 (pp20) outliers start: 82 outliers final: 51 residues processed: 244 average time/residue: 0.2555 time to fit residues: 95.3078 Evaluate side-chains 226 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 0.0020 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.0980 chunk 152 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16509 Z= 0.182 Angle : 0.711 14.794 22436 Z= 0.334 Chirality : 0.048 0.329 2940 Planarity : 0.004 0.055 2668 Dihedral : 9.418 83.335 4876 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer: Outliers : 3.77 % Allowed : 21.73 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.12 % 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: -1.52 (0.19), residues: 1777 helix: 1.09 (0.25), residues: 404 sheet: -0.98 (0.22), residues: 489 loop : -2.07 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 400 HIS 0.005 0.001 HIS A 72 PHE 0.009 0.001 PHE C 468 TYR 0.020 0.001 TYR B 643 ARG 0.010 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 192 time to evaluate : 1.692 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: B 530 MET cc_start: 0.9188 (ttm) cc_final: 0.8668 (ttm) REVERT: B 543 LEU cc_start: 0.9602 (mt) cc_final: 0.9155 (pp) REVERT: B 588 ARG cc_start: 0.9097 (ttm170) cc_final: 0.8559 (ttm170) REVERT: B 601 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8369 (mmtt) REVERT: B 643 TYR cc_start: 0.9233 (m-80) cc_final: 0.8925 (m-80) REVERT: C 80 ASN cc_start: 0.7601 (t0) cc_final: 0.7077 (t0) REVERT: C 95 MET cc_start: 0.8846 (ppp) cc_final: 0.8338 (ppp) REVERT: C 211 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 373 MET cc_start: 0.7869 (tmm) cc_final: 0.7665 (tmm) REVERT: D 591 GLN cc_start: 0.9262 (tt0) cc_final: 0.8816 (tm-30) REVERT: D 621 MET cc_start: 0.8415 (ppp) cc_final: 0.8126 (ppp) REVERT: D 629 MET cc_start: 0.7237 (mmm) cc_final: 0.6716 (mmm) REVERT: D 632 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8456 (mm-30) REVERT: E 95 MET cc_start: 0.9338 (ptt) cc_final: 0.9083 (ppp) REVERT: E 373 MET cc_start: 0.8786 (ptt) cc_final: 0.8195 (ptt) REVERT: E 426 MET cc_start: 0.7789 (mmm) cc_final: 0.7588 (tpp) REVERT: A 40 TYR cc_start: 0.8997 (t80) cc_final: 0.8271 (t80) REVERT: A 195 ASN cc_start: 0.8571 (m-40) cc_final: 0.7319 (t0) REVERT: A 240 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: A 269 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: A 373 MET cc_start: 0.7845 (ppp) cc_final: 0.7175 (ppp) REVERT: A 394 THR cc_start: 0.8898 (p) cc_final: 0.8672 (t) REVERT: A 449 ILE cc_start: 0.9411 (mt) cc_final: 0.9022 (mp) REVERT: A 475 MET cc_start: 0.9130 (tpp) cc_final: 0.8516 (tpp) REVERT: F 530 MET cc_start: 0.8521 (mtm) cc_final: 0.8120 (mtm) REVERT: F 566 LEU cc_start: 0.7117 (mt) cc_final: 0.6812 (mt) REVERT: F 575 GLN cc_start: 0.8894 (pt0) cc_final: 0.8344 (pp30) REVERT: F 618 THR cc_start: 0.9397 (m) cc_final: 0.9092 (p) REVERT: F 633 ARG cc_start: 0.9112 (mmm-85) cc_final: 0.8751 (mtp85) REVERT: F 648 GLU cc_start: 0.9407 (pp20) cc_final: 0.9171 (pp20) outliers start: 60 outliers final: 40 residues processed: 234 average time/residue: 0.2821 time to fit residues: 102.1178 Evaluate side-chains 214 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS D 575 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16509 Z= 0.350 Angle : 0.793 12.797 22436 Z= 0.378 Chirality : 0.050 0.333 2940 Planarity : 0.004 0.042 2668 Dihedral : 9.466 88.918 4876 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.45 % Favored : 90.43 % Rotamer: Outliers : 4.96 % Allowed : 21.98 % Favored : 73.05 % 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: -1.69 (0.19), residues: 1777 helix: 1.01 (0.26), residues: 395 sheet: -1.17 (0.22), residues: 501 loop : -2.14 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 69 HIS 0.009 0.002 HIS A 72 PHE 0.016 0.002 PHE A 382 TYR 0.019 0.002 TYR B 643 ARG 0.013 0.001 ARG D 633 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 171 time to evaluate : 1.852 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: B 530 MET cc_start: 0.9173 (ttm) cc_final: 0.8726 (ttm) REVERT: B 543 LEU cc_start: 0.9666 (mt) cc_final: 0.9162 (pp) REVERT: B 621 MET cc_start: 0.9198 (ptp) cc_final: 0.8991 (ptp) REVERT: B 643 TYR cc_start: 0.9364 (m-80) cc_final: 0.8859 (m-80) REVERT: C 80 ASN cc_start: 0.7518 (t0) cc_final: 0.6964 (t0) REVERT: C 107 ASP cc_start: 0.9756 (t70) cc_final: 0.9379 (t0) REVERT: C 133 ASP cc_start: 0.8619 (m-30) cc_final: 0.8047 (t70) REVERT: C 211 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 260 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8674 (mm) REVERT: C 426 MET cc_start: 0.8935 (mmm) cc_final: 0.8146 (mpp) REVERT: D 591 GLN cc_start: 0.9290 (tt0) cc_final: 0.8933 (pt0) REVERT: D 603 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8289 (pt) REVERT: D 621 MET cc_start: 0.8543 (ppp) cc_final: 0.8158 (ppp) REVERT: D 632 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8488 (mm-30) REVERT: E 373 MET cc_start: 0.8883 (ptt) cc_final: 0.8308 (ptt) REVERT: A 240 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8558 (ttpp) REVERT: A 373 MET cc_start: 0.7617 (ppp) cc_final: 0.7051 (ppp) REVERT: A 394 THR cc_start: 0.8881 (p) cc_final: 0.8660 (t) REVERT: A 475 MET cc_start: 0.9102 (tpp) cc_final: 0.8600 (tpp) REVERT: F 530 MET cc_start: 0.8549 (mtm) cc_final: 0.8249 (mtm) REVERT: F 575 GLN cc_start: 0.8925 (pt0) cc_final: 0.8398 (pp30) REVERT: F 577 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8750 (mm-40) REVERT: F 584 GLU cc_start: 0.8413 (mp0) cc_final: 0.8123 (mp0) REVERT: F 629 MET cc_start: 0.9026 (mmm) cc_final: 0.8799 (mmm) REVERT: F 633 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8831 (mtp85) outliers start: 79 outliers final: 58 residues processed: 229 average time/residue: 0.2400 time to fit residues: 85.3609 Evaluate side-chains 216 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16509 Z= 0.188 Angle : 0.716 11.825 22436 Z= 0.338 Chirality : 0.048 0.323 2940 Planarity : 0.004 0.040 2668 Dihedral : 8.968 85.946 4876 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.22 % Favored : 91.67 % Rotamer: Outliers : 3.58 % Allowed : 23.37 % Favored : 73.05 % 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: -1.43 (0.20), residues: 1777 helix: 1.29 (0.26), residues: 389 sheet: -0.92 (0.22), residues: 483 loop : -2.02 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 400 HIS 0.006 0.001 HIS F 564 PHE 0.008 0.001 PHE E 391 TYR 0.021 0.001 TYR B 643 ARG 0.008 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 183 time to evaluate : 1.406 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: 0.9145 (ttm) cc_final: 0.8806 (ttm) REVERT: B 543 LEU cc_start: 0.9688 (mt) cc_final: 0.9175 (pp) REVERT: B 588 ARG cc_start: 0.9073 (ttm170) cc_final: 0.8536 (ttm170) REVERT: B 601 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8424 (mmtt) REVERT: B 643 TYR cc_start: 0.9333 (m-80) cc_final: 0.8955 (m-80) REVERT: B 653 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: C 80 ASN cc_start: 0.7553 (t0) cc_final: 0.6984 (t0) REVERT: C 95 MET cc_start: 0.8879 (ppp) cc_final: 0.8344 (ppp) REVERT: C 107 ASP cc_start: 0.9688 (t70) cc_final: 0.9271 (t0) REVERT: C 133 ASP cc_start: 0.8631 (m-30) cc_final: 0.8093 (t70) REVERT: C 211 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 260 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8652 (mm) REVERT: C 388 THR cc_start: 0.8969 (p) cc_final: 0.8721 (t) REVERT: C 399 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6917 (p) REVERT: D 591 GLN cc_start: 0.9251 (tt0) cc_final: 0.8938 (pt0) REVERT: D 603 ILE cc_start: 0.8581 (tt) cc_final: 0.8300 (pt) REVERT: D 632 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8538 (mm-30) REVERT: E 373 MET cc_start: 0.8917 (ptt) cc_final: 0.8203 (ptt) REVERT: E 426 MET cc_start: 0.7658 (mmm) cc_final: 0.7446 (tpp) REVERT: A 40 TYR cc_start: 0.9024 (t80) cc_final: 0.8183 (t80) REVERT: A 195 ASN cc_start: 0.8631 (m-40) cc_final: 0.7537 (t0) REVERT: A 240 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8692 (pttp) REVERT: A 269 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: A 373 MET cc_start: 0.7921 (ppp) cc_final: 0.7375 (ppp) REVERT: A 394 THR cc_start: 0.8900 (p) cc_final: 0.8692 (t) REVERT: A 449 ILE cc_start: 0.9433 (mt) cc_final: 0.9017 (mp) REVERT: A 475 MET cc_start: 0.9110 (tpp) cc_final: 0.8637 (tpp) REVERT: F 575 GLN cc_start: 0.8922 (pt0) cc_final: 0.8361 (pp30) REVERT: F 584 GLU cc_start: 0.8553 (mp0) cc_final: 0.8311 (mp0) REVERT: F 633 ARG cc_start: 0.9202 (mmm-85) cc_final: 0.8838 (mtp85) outliers start: 57 outliers final: 43 residues processed: 228 average time/residue: 0.2417 time to fit residues: 85.7333 Evaluate side-chains 218 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16509 Z= 0.290 Angle : 0.762 11.655 22436 Z= 0.361 Chirality : 0.048 0.328 2940 Planarity : 0.004 0.037 2668 Dihedral : 8.960 89.633 4876 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.34 % Favored : 90.55 % Rotamer: Outliers : 3.52 % Allowed : 23.81 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.17 % 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: -1.58 (0.19), residues: 1777 helix: 1.11 (0.26), residues: 394 sheet: -0.96 (0.22), residues: 483 loop : -2.14 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 69 HIS 0.007 0.001 HIS A 72 PHE 0.012 0.001 PHE A 382 TYR 0.022 0.001 TYR D 586 ARG 0.009 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 170 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9184 (ttm) cc_final: 0.8814 (ttm) REVERT: B 588 ARG cc_start: 0.9110 (ttm170) cc_final: 0.8579 (ttm170) REVERT: B 643 TYR cc_start: 0.9368 (m-80) cc_final: 0.8746 (m-80) REVERT: C 80 ASN cc_start: 0.7589 (t0) cc_final: 0.6986 (t0) REVERT: C 107 ASP cc_start: 0.9750 (t70) cc_final: 0.9406 (t0) REVERT: C 133 ASP cc_start: 0.8631 (m-30) cc_final: 0.8143 (t70) REVERT: C 211 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 260 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8651 (mm) REVERT: C 388 THR cc_start: 0.8992 (p) cc_final: 0.8786 (t) REVERT: C 399 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7090 (p) REVERT: D 591 GLN cc_start: 0.9260 (tt0) cc_final: 0.8982 (pt0) REVERT: D 629 MET cc_start: 0.7976 (mmm) cc_final: 0.7711 (mmp) REVERT: D 632 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 195 ASN cc_start: 0.8639 (m-40) cc_final: 0.7352 (t0) REVERT: A 240 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8704 (pttp) REVERT: A 373 MET cc_start: 0.7839 (ppp) cc_final: 0.7237 (ppp) REVERT: A 394 THR cc_start: 0.8871 (p) cc_final: 0.8642 (t) REVERT: A 449 ILE cc_start: 0.9448 (mt) cc_final: 0.9043 (mp) REVERT: F 530 MET cc_start: 0.8186 (mtt) cc_final: 0.7401 (mmm) REVERT: F 575 GLN cc_start: 0.9064 (pt0) cc_final: 0.8426 (pp30) REVERT: F 577 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8901 (mm-40) REVERT: F 633 ARG cc_start: 0.9246 (mmm-85) cc_final: 0.8836 (mtp85) outliers start: 56 outliers final: 47 residues processed: 215 average time/residue: 0.2398 time to fit residues: 79.8696 Evaluate side-chains 212 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16509 Z= 0.294 Angle : 0.761 12.086 22436 Z= 0.366 Chirality : 0.049 0.330 2940 Planarity : 0.004 0.049 2668 Dihedral : 8.959 89.390 4876 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.51 % Favored : 90.38 % Rotamer: Outliers : 4.02 % Allowed : 23.37 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.17 % 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: -1.54 (0.19), residues: 1777 helix: 1.01 (0.26), residues: 388 sheet: -0.88 (0.23), residues: 462 loop : -2.06 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 69 HIS 0.006 0.001 HIS A 72 PHE 0.012 0.001 PHE A 382 TYR 0.022 0.001 TYR D 586 ARG 0.008 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 169 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9222 (ttm) cc_final: 0.8866 (ttm) REVERT: B 621 MET cc_start: 0.9229 (ptp) cc_final: 0.8600 (pmm) REVERT: B 643 TYR cc_start: 0.9401 (m-80) cc_final: 0.8875 (m-80) REVERT: C 80 ASN cc_start: 0.7477 (t0) cc_final: 0.6821 (t0) REVERT: C 107 ASP cc_start: 0.9749 (t70) cc_final: 0.9408 (t0) REVERT: C 133 ASP cc_start: 0.8420 (m-30) cc_final: 0.8038 (t70) REVERT: C 211 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 260 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8575 (mm) REVERT: C 399 THR cc_start: 0.7319 (OUTLIER) cc_final: 0.7090 (p) REVERT: D 591 GLN cc_start: 0.9227 (tt0) cc_final: 0.8930 (pt0) REVERT: D 605 THR cc_start: 0.9047 (p) cc_final: 0.8757 (t) REVERT: D 626 MET cc_start: 0.9079 (mmm) cc_final: 0.8789 (mmm) REVERT: D 632 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8625 (mm-30) REVERT: E 104 MET cc_start: 0.9317 (ttt) cc_final: 0.8815 (ttt) REVERT: E 373 MET cc_start: 0.8922 (ptt) cc_final: 0.8343 (ptm) REVERT: E 426 MET cc_start: 0.7810 (mmm) cc_final: 0.7564 (tpp) REVERT: A 240 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8579 (ttpp) REVERT: A 269 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: A 373 MET cc_start: 0.7885 (ppp) cc_final: 0.7325 (ppp) REVERT: A 394 THR cc_start: 0.8975 (p) cc_final: 0.8737 (t) REVERT: A 449 ILE cc_start: 0.9473 (mt) cc_final: 0.9066 (mp) REVERT: A 475 MET cc_start: 0.9175 (tpp) cc_final: 0.8608 (tpp) REVERT: F 530 MET cc_start: 0.8181 (mtt) cc_final: 0.7783 (mmm) REVERT: F 575 GLN cc_start: 0.9118 (pt0) cc_final: 0.8480 (pp30) REVERT: F 577 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8894 (mm-40) REVERT: F 584 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8365 (mt-10) REVERT: F 629 MET cc_start: 0.9250 (mmm) cc_final: 0.8939 (mmm) REVERT: F 633 ARG cc_start: 0.9278 (mmm-85) cc_final: 0.8861 (mtp85) outliers start: 64 outliers final: 48 residues processed: 219 average time/residue: 0.2474 time to fit residues: 83.4896 Evaluate side-chains 213 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 636 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16509 Z= 0.191 Angle : 0.729 12.425 22436 Z= 0.346 Chirality : 0.048 0.320 2940 Planarity : 0.004 0.041 2668 Dihedral : 8.684 87.700 4876 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.72 % Favored : 91.22 % Rotamer: Outliers : 3.08 % Allowed : 24.37 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.12 % 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: -1.43 (0.20), residues: 1777 helix: 1.13 (0.26), residues: 388 sheet: -0.74 (0.23), residues: 462 loop : -2.03 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 400 HIS 0.004 0.001 HIS F 564 PHE 0.007 0.001 PHE C 468 TYR 0.026 0.001 TYR D 586 ARG 0.010 0.000 ARG B 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 171 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9236 (ttm) cc_final: 0.8854 (ttm) REVERT: B 542 ARG cc_start: 0.9076 (tpt170) cc_final: 0.8152 (ttt180) REVERT: B 543 LEU cc_start: 0.9693 (mt) cc_final: 0.9088 (pp) REVERT: B 588 ARG cc_start: 0.9109 (ttm170) cc_final: 0.8646 (ttm170) REVERT: B 621 MET cc_start: 0.9182 (ptp) cc_final: 0.8516 (pmm) REVERT: B 643 TYR cc_start: 0.9386 (m-80) cc_final: 0.8965 (m-80) REVERT: B 653 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: C 71 THR cc_start: 0.8260 (t) cc_final: 0.8035 (p) REVERT: C 95 MET cc_start: 0.8844 (ppp) cc_final: 0.8313 (ppp) REVERT: C 107 ASP cc_start: 0.9710 (t70) cc_final: 0.9340 (t0) REVERT: C 133 ASP cc_start: 0.8423 (m-30) cc_final: 0.8042 (t70) REVERT: C 211 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 260 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8626 (mm) REVERT: C 399 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.7052 (p) REVERT: D 591 GLN cc_start: 0.9211 (tt0) cc_final: 0.8965 (pt0) REVERT: D 605 THR cc_start: 0.9089 (p) cc_final: 0.8793 (t) REVERT: D 626 MET cc_start: 0.9072 (mmm) cc_final: 0.8697 (mmm) REVERT: D 632 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8611 (mm-30) REVERT: E 104 MET cc_start: 0.9292 (ttt) cc_final: 0.8783 (ttt) REVERT: E 373 MET cc_start: 0.8901 (ptt) cc_final: 0.8317 (ptm) REVERT: E 426 MET cc_start: 0.7785 (mmm) cc_final: 0.7516 (tpp) REVERT: A 40 TYR cc_start: 0.9081 (t80) cc_final: 0.8189 (t80) REVERT: A 104 MET cc_start: 0.8914 (tmt) cc_final: 0.8668 (tmt) REVERT: A 195 ASN cc_start: 0.8499 (m-40) cc_final: 0.7204 (t0) REVERT: A 240 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8655 (pttp) REVERT: A 269 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: A 373 MET cc_start: 0.7941 (ppp) cc_final: 0.7338 (ppp) REVERT: A 394 THR cc_start: 0.8989 (p) cc_final: 0.8777 (t) REVERT: A 449 ILE cc_start: 0.9496 (mt) cc_final: 0.9125 (mp) REVERT: A 475 MET cc_start: 0.9175 (tpp) cc_final: 0.8603 (tpp) REVERT: F 530 MET cc_start: 0.8062 (mtt) cc_final: 0.7333 (mmm) REVERT: F 566 LEU cc_start: 0.7699 (mt) cc_final: 0.7341 (pp) REVERT: F 575 GLN cc_start: 0.9078 (pt0) cc_final: 0.8471 (pp30) REVERT: F 584 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8469 (mt-10) REVERT: F 626 MET cc_start: 0.8859 (ptp) cc_final: 0.8613 (pmm) REVERT: F 633 ARG cc_start: 0.9237 (mmm-85) cc_final: 0.8907 (mtp85) outliers start: 49 outliers final: 39 residues processed: 210 average time/residue: 0.2449 time to fit residues: 78.6565 Evaluate side-chains 208 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 636 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 139 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 17 optimal weight: 0.0270 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.8644 ------------------------------------------------------------------------------- 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058229 restraints weight = 64729.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060167 restraints weight = 35512.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061452 restraints weight = 24491.432| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16509 Z= 0.227 Angle : 0.744 13.108 22436 Z= 0.355 Chirality : 0.048 0.331 2940 Planarity : 0.004 0.046 2668 Dihedral : 8.609 87.610 4876 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.12 % Favored : 90.77 % Rotamer: Outliers : 2.83 % Allowed : 24.81 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.17 % 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: -1.46 (0.20), residues: 1777 helix: 1.06 (0.26), residues: 388 sheet: -0.74 (0.23), residues: 462 loop : -2.04 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 400 HIS 0.003 0.001 HIS E 330 PHE 0.008 0.001 PHE A 382 TYR 0.027 0.001 TYR D 586 ARG 0.010 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.79 seconds wall clock time: 58 minutes 5.75 seconds (3485.75 seconds total)