Starting phenix.real_space_refine on Wed Apr 10 19:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/04_2024/6crq_7568.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/04_2024/6crq_7568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/04_2024/6crq_7568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/04_2024/6crq_7568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/04_2024/6crq_7568.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/04_2024/6crq_7568.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 12702 2.51 5 N 3399 2.21 5 O 4047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20271 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3537 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "B" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3537 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "F" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3537 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "M" 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "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: 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 Chain: "H" 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: 10.24, per 1000 atoms: 0.51 Number of scatterers: 20271 At special positions: 0 Unit cell: (146.88, 140.76, 119.34, 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 123 16.00 O 4047 8.00 N 3399 7.00 C 12702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.19 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.14 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.17 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.06 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.25 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.11 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.70 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.53 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS G 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.08 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.17 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.10 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.06 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.22 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS H 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=1.92 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA a 3 " - " MAN a 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG 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 s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 807 " - " ASN A 160 " " NAG A 818 " - " ASN A 234 " " NAG A 832 " - " ASN A 339 " " NAG B 807 " - " ASN B 160 " " NAG B 818 " - " ASN B 234 " " NAG B 832 " - " ASN B 339 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 611 " " NAG F 807 " - " ASN F 160 " " NAG F 818 " - " ASN F 234 " " NAG F 832 " - " ASN F 339 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 611 " " NAG H 701 " - " ASN H 637 " " NAG H 702 " - " ASN H 618 " " NAG H 703 " - " ASN H 611 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 363 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN A 88 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN B 262 " " NAG Z 1 " - " ASN B 448 " " NAG a 1 " - " ASN B 276 " " NAG b 1 " - " ASN B 295 " " NAG c 1 " - " ASN B 386 " " NAG d 1 " - " ASN B 363 " " NAG e 1 " - " ASN B 197 " " NAG f 1 " - " ASN B 133 " " NAG g 1 " - " ASN B 156 " " NAG h 1 " - " ASN B 301 " " NAG i 1 " - " ASN B 88 " " NAG j 1 " - " ASN B 332 " " NAG k 1 " - " ASN F 262 " " NAG l 1 " - " ASN F 448 " " NAG m 1 " - " ASN F 276 " " NAG n 1 " - " ASN F 295 " " NAG o 1 " - " ASN F 386 " " NAG p 1 " - " ASN F 363 " " NAG q 1 " - " ASN F 197 " " NAG r 1 " - " ASN F 133 " " NAG s 1 " - " ASN F 156 " " NAG t 1 " - " ASN F 301 " " NAG u 1 " - " ASN F 88 " " NAG v 1 " - " ASN F 332 " Time building additional restraints: 9.52 Conformation dependent library (CDL) restraints added in 3.4 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.518A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.888A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.811A pdb=" N PHE A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.844A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.527A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.576A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 543 Processing helix chain 'C' and resid 574 through 597 Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.534A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 Processing helix chain 'C' and resid 650 through 663 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 77 through 83 Proline residue: E 80 - end of helix Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.910A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.848A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.789A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.569A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 Processing helix chain 'G' and resid 529 through 534 removed outlier: 3.604A pdb=" N SER G 534 " --> pdb=" O MET G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 Processing helix chain 'G' and resid 574 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.739A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.741A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'I' and resid 25 through 32 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 27 through 31 No H-bonds generated for 'chain 'K' and resid 27 through 31' Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing helix chain 'F' and resid 57 through 64 removed outlier: 3.822A pdb=" N TYR F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.821A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.832A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.561A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 removed outlier: 3.823A pdb=" N SER H 534 " --> pdb=" O MET H 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 543 Processing helix chain 'H' and resid 574 through 597 Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 626 removed outlier: 3.693A pdb=" N MET H 626 " --> pdb=" O ILE H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 636 removed outlier: 4.083A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 650 removed outlier: 3.555A pdb=" N GLN H 650 " --> pdb=" O LEU H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 663 Processing helix chain 'J' and resid 25 through 30 Processing helix chain 'J' and resid 60 through 66 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.926A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.695A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.524A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.946A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.183A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.631A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 284 through 285 removed outlier: 6.271A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 308 removed outlier: 4.737A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.646A pdb=" N ILE D 35 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP D 50 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.606A pdb=" N CYS D 92 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.439A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.439A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.617A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 44 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 494 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 42 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N VAL B 496 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N TYR B 40 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL B 38 " --> pdb=" O PRO B 498 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL G 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL B 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR G 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR B 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS G 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AC2, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.300A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 274 removed outlier: 4.186A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 302 through 308 removed outlier: 4.705A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.684A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.636A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.068A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.068A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 496 through 499 removed outlier: 4.907A pdb=" N VAL F 36 " --> pdb=" O THR H 606 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.138A pdb=" N VAL F 44 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AD8, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'F' and resid 175 through 177 removed outlier: 4.001A pdb=" N THR F 132 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER F 158 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.185A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.375A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 284 through 285 removed outlier: 6.160A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 302 through 308 removed outlier: 4.707A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.626A pdb=" N ILE J 35 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP J 50 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.692A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.690A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 11 through 12 749 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5700 1.33 - 1.47: 5920 1.47 - 1.60: 8884 1.60 - 1.73: 1 1.73 - 1.86: 168 Bond restraints: 20673 Sorted by residual: bond pdb=" C ASN A 300 " pdb=" N ASN A 301 " ideal model delta sigma weight residual 1.333 1.435 -0.102 1.45e-02 4.76e+03 4.96e+01 bond pdb=" C ASN F 300 " pdb=" N ASN F 301 " ideal model delta sigma weight residual 1.333 1.435 -0.102 1.45e-02 4.76e+03 4.93e+01 bond pdb=" C GLU A 87 " pdb=" N ASN A 88 " ideal model delta sigma weight residual 1.333 1.251 0.082 1.39e-02 5.18e+03 3.51e+01 bond pdb=" CB LEU E 47 " pdb=" CG LEU E 47 " ideal model delta sigma weight residual 1.530 1.430 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " ideal model delta sigma weight residual 1.497 1.432 0.065 1.40e-02 5.10e+03 2.15e+01 ... (remaining 20668 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.33: 446 105.33 - 112.52: 10929 112.52 - 119.71: 6828 119.71 - 126.90: 9576 126.90 - 134.09: 256 Bond angle restraints: 28035 Sorted by residual: angle pdb=" N VAL B 172 " pdb=" CA VAL B 172 " pdb=" C VAL B 172 " ideal model delta sigma weight residual 110.72 121.07 -10.35 1.01e+00 9.80e-01 1.05e+02 angle pdb=" C ARG B 298 " pdb=" N PRO B 299 " pdb=" CA PRO B 299 " ideal model delta sigma weight residual 120.31 130.04 -9.73 9.80e-01 1.04e+00 9.86e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 120.31 129.56 -9.25 9.80e-01 1.04e+00 8.91e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 120.31 129.54 -9.23 9.80e-01 1.04e+00 8.86e+01 angle pdb=" N ALA H 525 " pdb=" CA ALA H 525 " pdb=" C ALA H 525 " ideal model delta sigma weight residual 111.28 120.89 -9.61 1.09e+00 8.42e-01 7.78e+01 ... (remaining 28030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 13124 21.82 - 43.63: 374 43.63 - 65.45: 116 65.45 - 87.27: 68 87.27 - 109.08: 37 Dihedral angle restraints: 13719 sinusoidal: 6867 harmonic: 6852 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual 93.00 48.42 44.58 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.42 44.42 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS F 131 " pdb=" SG CYS F 131 " pdb=" SG CYS F 157 " pdb=" CB CYS F 157 " ideal model delta sinusoidal sigma weight residual 93.00 50.73 42.27 1 1.00e+01 1.00e-02 2.50e+01 ... (remaining 13716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3099 0.133 - 0.266: 299 0.266 - 0.399: 15 0.399 - 0.532: 12 0.532 - 0.665: 7 Chirality restraints: 3432 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 -2.59 0.19 2.00e-02 2.50e+03 9.50e+01 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 -2.59 0.19 2.00e-02 2.50e+03 8.69e+01 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.48e+01 ... (remaining 3429 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 611 " -0.147 2.00e-02 2.50e+03 1.54e-01 2.97e+02 pdb=" CG ASN H 611 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN H 611 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN H 611 " 0.241 2.00e-02 2.50e+03 pdb=" C1 NAG H 703 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 611 " -0.142 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN G 611 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN G 611 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN G 611 " 0.235 2.00e-02 2.50e+03 pdb=" C1 NAG G 703 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.129 2.00e-02 2.50e+03 1.34e-01 2.25e+02 pdb=" CG ASN A 332 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.210 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.158 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 51 2.45 - 3.06: 13918 3.06 - 3.68: 27741 3.68 - 4.29: 44655 4.29 - 4.90: 70874 Nonbonded interactions: 157239 Sorted by model distance: nonbonded pdb=" C8 NAG r 1 " pdb=" O3 NAG r 1 " model vdw 1.839 3.460 nonbonded pdb=" O3 NAG m 2 " pdb=" O7 NAG m 2 " model vdw 1.865 2.440 nonbonded pdb=" O3 NAG A 807 " pdb=" O7 NAG A 807 " model vdw 1.866 2.440 nonbonded pdb=" C8 NAG f 1 " pdb=" O3 NAG f 1 " model vdw 1.867 3.460 nonbonded pdb=" O3 NAG F 807 " pdb=" O7 NAG F 807 " model vdw 1.868 2.440 ... (remaining 157234 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 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Y' selection = chain 'a' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'S' selection = chain 'e' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.990 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 54.980 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.440 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.015 0.112 20673 Z= 0.954 Angle : 1.498 12.288 28035 Z= 0.958 Chirality : 0.087 0.665 3432 Planarity : 0.007 0.076 3432 Dihedral : 14.008 109.081 9195 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 1.59 % Favored : 97.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: 1.77 (0.17), residues: 2343 helix: -0.15 (0.22), residues: 459 sheet: 1.14 (0.21), residues: 591 loop : 2.00 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.007 TRP G 610 HIS 0.008 0.002 HIS K 32 PHE 0.021 0.004 PHE L 98 TYR 0.051 0.005 TYR A 173 ARG 0.004 0.001 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 732 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8828 (m-40) cc_final: 0.8019 (p0) REVERT: A 104 MET cc_start: 0.8541 (ttt) cc_final: 0.8221 (tpp) REVERT: A 207 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7323 (ptpt) REVERT: A 295 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6351 (t0) REVERT: A 348 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8448 (mm-40) REVERT: A 443 ILE cc_start: 0.8267 (mm) cc_final: 0.7847 (mm) REVERT: C 530 MET cc_start: 0.7554 (mtp) cc_final: 0.7106 (mtp) REVERT: C 618 ASN cc_start: 0.6334 (OUTLIER) cc_final: 0.6013 (m-40) REVERT: C 635 ILE cc_start: 0.8963 (pt) cc_final: 0.8678 (pt) REVERT: D 76 PHE cc_start: 0.8550 (m-80) cc_final: 0.8196 (m-10) REVERT: D 80 MET cc_start: 0.8823 (ttp) cc_final: 0.8575 (ttt) REVERT: E 6 GLN cc_start: 0.7046 (mt0) cc_final: 0.6681 (mt0) REVERT: E 23 CYS cc_start: 0.4025 (p) cc_final: 0.3363 (p) REVERT: E 54 ARG cc_start: 0.7310 (mtt180) cc_final: 0.7062 (ttm-80) REVERT: B 38 VAL cc_start: 0.8835 (t) cc_final: 0.8584 (p) REVERT: B 97 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8119 (ttmt) REVERT: B 104 MET cc_start: 0.8596 (ttt) cc_final: 0.8143 (tpp) REVERT: B 348 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8686 (mm-40) REVERT: B 442 VAL cc_start: 0.7869 (t) cc_final: 0.7585 (p) REVERT: G 530 MET cc_start: 0.7777 (mtp) cc_final: 0.7488 (mtp) REVERT: I 32 THR cc_start: 0.8574 (m) cc_final: 0.8373 (p) REVERT: I 73 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7670 (mtp85) REVERT: K 42 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8214 (mp10) REVERT: K 102 THR cc_start: 0.7806 (p) cc_final: 0.7436 (p) REVERT: F 38 VAL cc_start: 0.8966 (t) cc_final: 0.8711 (t) REVERT: F 98 ASN cc_start: 0.8138 (t0) cc_final: 0.7521 (t0) REVERT: F 99 ASN cc_start: 0.8531 (m-40) cc_final: 0.8006 (p0) REVERT: F 100 MET cc_start: 0.7960 (mtp) cc_final: 0.7388 (ttm) REVERT: F 104 MET cc_start: 0.8512 (ttt) cc_final: 0.8117 (tpp) REVERT: F 178 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8180 (ttm-80) REVERT: F 194 ILE cc_start: 0.9089 (tt) cc_final: 0.8884 (tt) REVERT: F 328 GLN cc_start: 0.8464 (tt0) cc_final: 0.8061 (mp10) REVERT: F 442 VAL cc_start: 0.7536 (t) cc_final: 0.7211 (p) REVERT: F 474 ASP cc_start: 0.7139 (t0) cc_final: 0.6714 (p0) REVERT: H 530 MET cc_start: 0.7724 (mtp) cc_final: 0.7022 (mtp) REVERT: H 618 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6393 (m-40) REVERT: H 634 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7299 (tp30) REVERT: J 24 THR cc_start: 0.7555 (t) cc_final: 0.7308 (t) REVERT: J 25 SER cc_start: 0.8382 (t) cc_final: 0.7922 (p) REVERT: J 87 THR cc_start: 0.8650 (m) cc_final: 0.8275 (p) REVERT: L 30 TYR cc_start: 0.7574 (m-80) cc_final: 0.7157 (m-80) REVERT: L 102 THR cc_start: 0.7881 (p) cc_final: 0.7480 (t) outliers start: 22 outliers final: 4 residues processed: 746 average time/residue: 0.3688 time to fit residues: 400.9924 Evaluate side-chains 375 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 367 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 99 ASN A 283 ASN A 425 ASN A 440 GLN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 6 GLN B 425 ASN G 540 GLN G 590 GLN G 625 ASN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 95 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 425 ASN H 543 ASN J 1 GLN J 6 GLN J 79 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20673 Z= 0.225 Angle : 0.819 14.920 28035 Z= 0.402 Chirality : 0.051 0.483 3432 Planarity : 0.005 0.079 3432 Dihedral : 9.950 75.114 4734 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.29 % Allowed : 2.98 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.39 (0.17), residues: 2343 helix: 0.81 (0.24), residues: 435 sheet: 0.71 (0.20), residues: 645 loop : 1.31 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 479 HIS 0.005 0.001 HIS E 32 PHE 0.023 0.002 PHE E 49 TYR 0.022 0.002 TYR A 173 ARG 0.007 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 518 time to evaluate : 2.233 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: A 49 GLU cc_start: 0.7066 (mp0) cc_final: 0.6750 (mm-30) REVERT: A 51 THR cc_start: 0.8908 (m) cc_final: 0.8630 (p) REVERT: A 84 ILE cc_start: 0.7317 (mp) cc_final: 0.7100 (mm) REVERT: A 207 LYS cc_start: 0.7827 (mmmt) cc_final: 0.7592 (ptpt) REVERT: A 256 SER cc_start: 0.8809 (p) cc_final: 0.8519 (m) REVERT: A 328 GLN cc_start: 0.8416 (tt0) cc_final: 0.7991 (pt0) REVERT: C 530 MET cc_start: 0.7312 (mtp) cc_final: 0.6955 (mtp) REVERT: C 543 ASN cc_start: 0.8185 (t0) cc_final: 0.7930 (t0) REVERT: C 648 GLU cc_start: 0.9017 (pt0) cc_final: 0.8381 (pt0) REVERT: D 31 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8113 (mtt-85) REVERT: D 82 ILE cc_start: 0.9080 (mm) cc_final: 0.8839 (mm) REVERT: E 42 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8257 (mp10) REVERT: E 54 ARG cc_start: 0.7455 (mtt180) cc_final: 0.7209 (ttm170) REVERT: E 102 THR cc_start: 0.7805 (p) cc_final: 0.7405 (t) REVERT: B 97 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8319 (ttpt) REVERT: B 100 MET cc_start: 0.7819 (ptm) cc_final: 0.7427 (ttm) REVERT: B 194 ILE cc_start: 0.9142 (tt) cc_final: 0.8934 (tt) REVERT: B 257 THR cc_start: 0.8784 (p) cc_final: 0.8314 (p) REVERT: B 442 VAL cc_start: 0.7838 (t) cc_final: 0.7481 (p) REVERT: G 530 MET cc_start: 0.7788 (mtp) cc_final: 0.7091 (mmm) REVERT: G 621 GLU cc_start: 0.7295 (tm-30) cc_final: 0.7092 (tm-30) REVERT: G 648 GLU cc_start: 0.8954 (pt0) cc_final: 0.8749 (pt0) REVERT: I 31 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8529 (mtm-85) REVERT: I 100 PHE cc_start: 0.7977 (m-80) cc_final: 0.7661 (m-10) REVERT: K 42 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8202 (mp10) REVERT: K 77 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7171 (ttp80) REVERT: F 84 ILE cc_start: 0.8054 (mp) cc_final: 0.7635 (mp) REVERT: F 99 ASN cc_start: 0.8190 (m-40) cc_final: 0.7810 (m-40) REVERT: F 100 MET cc_start: 0.7863 (mtp) cc_final: 0.7640 (mtp) REVERT: F 103 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: F 104 MET cc_start: 0.8218 (ttt) cc_final: 0.7844 (tpp) REVERT: F 161 MET cc_start: 0.7626 (tpt) cc_final: 0.6967 (tpt) REVERT: F 195 ASN cc_start: 0.8682 (t0) cc_final: 0.8352 (t0) REVERT: F 328 GLN cc_start: 0.8525 (tt0) cc_final: 0.8108 (tp40) REVERT: F 341 THR cc_start: 0.9256 (p) cc_final: 0.8918 (t) REVERT: F 502 LYS cc_start: 0.6296 (tppt) cc_final: 0.5370 (tptt) REVERT: H 530 MET cc_start: 0.7563 (mtp) cc_final: 0.7200 (mtm) REVERT: H 620 SER cc_start: 0.8609 (p) cc_final: 0.8402 (p) REVERT: H 621 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6979 (tm-30) REVERT: H 628 TRP cc_start: 0.7454 (m100) cc_final: 0.7233 (m100) REVERT: H 648 GLU cc_start: 0.8647 (pt0) cc_final: 0.8160 (pt0) REVERT: J 6 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8378 (tp40) REVERT: J 31 ARG cc_start: 0.8742 (tpp80) cc_final: 0.8364 (mtt-85) REVERT: J 87 THR cc_start: 0.8802 (m) cc_final: 0.8467 (p) REVERT: J 102 LEU cc_start: 0.8171 (mp) cc_final: 0.7782 (mp) REVERT: L 30 TYR cc_start: 0.7790 (m-80) cc_final: 0.7314 (m-80) REVERT: L 96 GLU cc_start: 0.8549 (pt0) cc_final: 0.8328 (pt0) REVERT: L 102 THR cc_start: 0.7777 (p) cc_final: 0.7563 (p) outliers start: 6 outliers final: 2 residues processed: 523 average time/residue: 0.3252 time to fit residues: 260.1388 Evaluate side-chains 345 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 341 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 146 optimal weight: 0.0170 chunk 59 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 232 optimal weight: 0.0170 chunk 192 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS G 607 ASN G 650 GLN I 6 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20673 Z= 0.209 Angle : 0.725 15.284 28035 Z= 0.355 Chirality : 0.049 0.483 3432 Planarity : 0.004 0.042 3432 Dihedral : 7.501 58.588 4734 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: 1.23 (0.17), residues: 2343 helix: 1.38 (0.25), residues: 414 sheet: 0.62 (0.20), residues: 657 loop : 0.93 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 610 HIS 0.004 0.001 HIS F 66 PHE 0.025 0.002 PHE I 63 TYR 0.018 0.001 TYR J 98 ARG 0.008 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 2.276 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: A 51 THR cc_start: 0.8951 (m) cc_final: 0.8723 (p) REVERT: A 207 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7553 (ptpt) REVERT: A 271 MET cc_start: 0.8296 (mmp) cc_final: 0.7802 (mmm) REVERT: A 328 GLN cc_start: 0.8581 (tt0) cc_final: 0.8196 (pt0) REVERT: C 543 ASN cc_start: 0.8171 (t0) cc_final: 0.7966 (t0) REVERT: C 645 LEU cc_start: 0.8708 (mt) cc_final: 0.8456 (mt) REVERT: C 648 GLU cc_start: 0.8982 (pt0) cc_final: 0.8365 (pt0) REVERT: C 649 SER cc_start: 0.8582 (m) cc_final: 0.8362 (p) REVERT: D 25 SER cc_start: 0.7707 (m) cc_final: 0.7470 (p) REVERT: D 73 ARG cc_start: 0.8505 (ptp-110) cc_final: 0.8204 (mtp85) REVERT: D 107 THR cc_start: 0.9088 (t) cc_final: 0.8827 (t) REVERT: E 23 CYS cc_start: 0.3183 (p) cc_final: 0.2952 (p) REVERT: E 42 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8260 (mp10) REVERT: E 88 CYS cc_start: 0.6515 (m) cc_final: 0.6058 (m) REVERT: B 97 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8298 (ttpt) REVERT: B 103 GLN cc_start: 0.7889 (mt0) cc_final: 0.7191 (tm-30) REVERT: B 104 MET cc_start: 0.8321 (ttt) cc_final: 0.8092 (tpp) REVERT: B 107 ASP cc_start: 0.8485 (m-30) cc_final: 0.6803 (m-30) REVERT: B 442 VAL cc_start: 0.7666 (t) cc_final: 0.7271 (p) REVERT: G 530 MET cc_start: 0.7930 (mtp) cc_final: 0.6792 (mmm) REVERT: G 621 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6719 (tm-30) REVERT: G 648 GLU cc_start: 0.8923 (pt0) cc_final: 0.8564 (pt0) REVERT: I 31 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8533 (mtm-85) REVERT: I 73 ARG cc_start: 0.8218 (ptp-110) cc_final: 0.7432 (mtp85) REVERT: K 36 TYR cc_start: 0.8858 (m-80) cc_final: 0.8594 (m-10) REVERT: K 71 TYR cc_start: 0.6511 (t80) cc_final: 0.6267 (t80) REVERT: K 86 TYR cc_start: 0.8705 (m-80) cc_final: 0.8444 (m-10) REVERT: F 53 PHE cc_start: 0.7609 (m-10) cc_final: 0.7292 (m-10) REVERT: F 64 GLU cc_start: 0.6457 (tm-30) cc_final: 0.5661 (tm-30) REVERT: F 104 MET cc_start: 0.8403 (ttt) cc_final: 0.7946 (tpp) REVERT: F 161 MET cc_start: 0.7714 (tpt) cc_final: 0.7097 (tpt) REVERT: F 195 ASN cc_start: 0.8584 (t0) cc_final: 0.8194 (t0) REVERT: F 328 GLN cc_start: 0.8550 (tt0) cc_final: 0.8185 (mp10) REVERT: H 530 MET cc_start: 0.7687 (mtp) cc_final: 0.6349 (mmm) REVERT: H 589 ASP cc_start: 0.8682 (t0) cc_final: 0.8475 (t0) REVERT: H 621 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7012 (tm-30) REVERT: H 648 GLU cc_start: 0.8551 (pt0) cc_final: 0.8267 (pt0) REVERT: L 12 SER cc_start: 0.6931 (t) cc_final: 0.6290 (m) REVERT: L 13 LEU cc_start: 0.7356 (tt) cc_final: 0.5627 (tt) REVERT: L 18 THR cc_start: 0.5966 (m) cc_final: 0.5659 (t) REVERT: L 30 TYR cc_start: 0.7718 (m-80) cc_final: 0.7280 (m-80) REVERT: L 42 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8391 (mp10) REVERT: L 102 THR cc_start: 0.7603 (p) cc_final: 0.7144 (p) outliers start: 1 outliers final: 1 residues processed: 460 average time/residue: 0.3130 time to fit residues: 222.4252 Evaluate side-chains 320 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN D 6 GLN B 170 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 625 ASN J 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20673 Z= 0.375 Angle : 0.827 14.475 28035 Z= 0.404 Chirality : 0.051 0.379 3432 Planarity : 0.005 0.055 3432 Dihedral : 7.408 59.539 4734 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2343 helix: 0.98 (0.25), residues: 432 sheet: 0.44 (0.20), residues: 654 loop : 0.13 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 631 HIS 0.010 0.002 HIS E 32 PHE 0.022 0.002 PHE B 176 TYR 0.025 0.002 TYR D 100E ARG 0.007 0.001 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 389 time to evaluate : 2.108 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: A 271 MET cc_start: 0.8257 (mmp) cc_final: 0.7944 (mmm) REVERT: C 536 THR cc_start: 0.8669 (m) cc_final: 0.8327 (m) REVERT: C 648 GLU cc_start: 0.9017 (pt0) cc_final: 0.8775 (pt0) REVERT: E 23 CYS cc_start: 0.3603 (p) cc_final: 0.2645 (p) REVERT: E 42 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8230 (mp10) REVERT: B 97 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8544 (mtmt) REVERT: B 104 MET cc_start: 0.8547 (ttt) cc_final: 0.8307 (tpp) REVERT: B 107 ASP cc_start: 0.8615 (m-30) cc_final: 0.7857 (t0) REVERT: B 108 ILE cc_start: 0.9014 (mt) cc_final: 0.8629 (mm) REVERT: G 530 MET cc_start: 0.7763 (mtp) cc_final: 0.7184 (mmm) REVERT: G 538 THR cc_start: 0.8848 (t) cc_final: 0.8619 (m) REVERT: G 543 ASN cc_start: 0.8093 (t0) cc_final: 0.7874 (t0) REVERT: G 621 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7004 (tm-30) REVERT: G 626 MET cc_start: 0.7391 (tmm) cc_final: 0.6730 (ppp) REVERT: G 648 GLU cc_start: 0.9064 (pt0) cc_final: 0.8726 (pt0) REVERT: G 650 GLN cc_start: 0.6861 (tp40) cc_final: 0.5695 (tp40) REVERT: I 31 ARG cc_start: 0.8998 (ttm110) cc_final: 0.8624 (mtp-110) REVERT: K 71 TYR cc_start: 0.6682 (t80) cc_final: 0.6080 (t80) REVERT: F 64 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6055 (tm-30) REVERT: F 161 MET cc_start: 0.7803 (tpt) cc_final: 0.7447 (tpt) REVERT: F 271 MET cc_start: 0.8261 (mmm) cc_final: 0.8046 (mmm) REVERT: F 328 GLN cc_start: 0.8701 (tt0) cc_final: 0.8240 (mp10) REVERT: H 530 MET cc_start: 0.7797 (mtp) cc_final: 0.7326 (mmm) REVERT: H 589 ASP cc_start: 0.8743 (t0) cc_final: 0.8459 (t0) REVERT: H 621 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7200 (tm-30) REVERT: H 626 MET cc_start: 0.7285 (tmm) cc_final: 0.6367 (tmm) REVERT: J 6 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: L 12 SER cc_start: 0.7306 (t) cc_final: 0.6776 (m) REVERT: L 18 THR cc_start: 0.5886 (m) cc_final: 0.5554 (t) REVERT: L 96 GLU cc_start: 0.8445 (pt0) cc_final: 0.8214 (pt0) REVERT: L 102 THR cc_start: 0.8158 (p) cc_final: 0.7802 (p) outliers start: 2 outliers final: 1 residues processed: 391 average time/residue: 0.3032 time to fit residues: 187.8435 Evaluate side-chains 292 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.0570 chunk 205 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20673 Z= 0.192 Angle : 0.678 12.800 28035 Z= 0.330 Chirality : 0.047 0.416 3432 Planarity : 0.004 0.044 3432 Dihedral : 7.089 59.630 4734 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2343 helix: 1.31 (0.26), residues: 420 sheet: 0.64 (0.20), residues: 657 loop : 0.09 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 610 HIS 0.004 0.001 HIS E 32 PHE 0.029 0.002 PHE D 76 TYR 0.018 0.001 TYR J 100E ARG 0.005 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 434 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8594 (ttt) cc_final: 0.8286 (tpp) REVERT: A 254 VAL cc_start: 0.8788 (t) cc_final: 0.8586 (m) REVERT: A 256 SER cc_start: 0.8823 (p) cc_final: 0.8437 (m) REVERT: C 536 THR cc_start: 0.8522 (m) cc_final: 0.8143 (m) REVERT: C 634 GLU cc_start: 0.8212 (tp30) cc_final: 0.7944 (tp30) REVERT: C 648 GLU cc_start: 0.9020 (pt0) cc_final: 0.8511 (pp20) REVERT: C 649 SER cc_start: 0.8792 (m) cc_final: 0.7609 (p) REVERT: C 650 GLN cc_start: 0.7008 (mm110) cc_final: 0.6324 (mm110) REVERT: C 655 LYS cc_start: 0.7671 (mttm) cc_final: 0.7070 (mtmm) REVERT: E 23 CYS cc_start: 0.3311 (p) cc_final: 0.3020 (p) REVERT: B 35 TRP cc_start: 0.7627 (m-90) cc_final: 0.7169 (m-90) REVERT: B 97 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8569 (mtmt) REVERT: B 103 GLN cc_start: 0.6592 (tm-30) cc_final: 0.5846 (tm-30) REVERT: B 104 MET cc_start: 0.8744 (ttt) cc_final: 0.8292 (tpp) REVERT: B 107 ASP cc_start: 0.7848 (m-30) cc_final: 0.7175 (m-30) REVERT: B 108 ILE cc_start: 0.8992 (mt) cc_final: 0.8681 (mm) REVERT: G 530 MET cc_start: 0.7782 (mtp) cc_final: 0.7318 (mmm) REVERT: G 538 THR cc_start: 0.8836 (t) cc_final: 0.8546 (m) REVERT: G 543 ASN cc_start: 0.8058 (t0) cc_final: 0.7844 (t0) REVERT: G 621 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7001 (tm-30) REVERT: G 626 MET cc_start: 0.7334 (tmm) cc_final: 0.7078 (ppp) REVERT: G 648 GLU cc_start: 0.8914 (pt0) cc_final: 0.8662 (pt0) REVERT: G 650 GLN cc_start: 0.6546 (tp40) cc_final: 0.5087 (tp40) REVERT: I 6 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8653 (tp40) REVERT: I 31 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8490 (mtp-110) REVERT: I 107 THR cc_start: 0.9232 (t) cc_final: 0.8982 (m) REVERT: I 109 ILE cc_start: 0.9449 (mm) cc_final: 0.9235 (mm) REVERT: K 71 TYR cc_start: 0.6551 (t80) cc_final: 0.6123 (t80) REVERT: K 86 TYR cc_start: 0.8783 (m-80) cc_final: 0.8302 (m-10) REVERT: F 84 ILE cc_start: 0.7475 (mp) cc_final: 0.7223 (mm) REVERT: F 100 MET cc_start: 0.8188 (mtp) cc_final: 0.7753 (mtp) REVERT: F 104 MET cc_start: 0.8585 (ttt) cc_final: 0.8261 (tpp) REVERT: F 116 LEU cc_start: 0.8405 (tt) cc_final: 0.7579 (tt) REVERT: F 161 MET cc_start: 0.7693 (tpt) cc_final: 0.7385 (tpt) REVERT: F 195 ASN cc_start: 0.8396 (t0) cc_final: 0.7981 (t0) REVERT: F 328 GLN cc_start: 0.8688 (tt0) cc_final: 0.8257 (mp10) REVERT: F 502 LYS cc_start: 0.5884 (tppt) cc_final: 0.5241 (tptt) REVERT: H 539 VAL cc_start: 0.8236 (t) cc_final: 0.8028 (t) REVERT: H 542 ARG cc_start: 0.5751 (ttt-90) cc_final: 0.5471 (ttp-110) REVERT: H 589 ASP cc_start: 0.8663 (t0) cc_final: 0.8447 (t0) REVERT: H 606 THR cc_start: 0.8923 (p) cc_final: 0.8389 (p) REVERT: H 621 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7214 (tm-30) REVERT: H 626 MET cc_start: 0.7048 (tmm) cc_final: 0.5929 (tmm) REVERT: L 12 SER cc_start: 0.7544 (t) cc_final: 0.7205 (m) REVERT: L 30 TYR cc_start: 0.7791 (m-80) cc_final: 0.7359 (m-80) REVERT: L 102 THR cc_start: 0.8020 (p) cc_final: 0.7617 (p) outliers start: 1 outliers final: 0 residues processed: 435 average time/residue: 0.3079 time to fit residues: 210.1261 Evaluate side-chains 303 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 43 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS G 540 GLN ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 43 GLN K 70 GLN H 543 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 GLN J 6 GLN J 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 20673 Z= 0.547 Angle : 0.932 11.962 28035 Z= 0.459 Chirality : 0.054 0.345 3432 Planarity : 0.006 0.069 3432 Dihedral : 8.782 59.571 4734 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2343 helix: -0.13 (0.23), residues: 450 sheet: -0.08 (0.21), residues: 594 loop : -0.80 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP G 610 HIS 0.012 0.003 HIS E 32 PHE 0.027 0.003 PHE B 176 TYR 0.027 0.003 TYR K 71 ARG 0.010 0.001 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7095 (m-90) cc_final: 0.6786 (m-90) REVERT: A 217 TYR cc_start: 0.8444 (m-80) cc_final: 0.7926 (m-80) REVERT: C 645 LEU cc_start: 0.8675 (mt) cc_final: 0.8436 (mt) REVERT: C 648 GLU cc_start: 0.9022 (pt0) cc_final: 0.8386 (pt0) REVERT: C 650 GLN cc_start: 0.7093 (tp40) cc_final: 0.6610 (tp-100) REVERT: E 23 CYS cc_start: 0.3511 (p) cc_final: 0.3079 (p) REVERT: E 42 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8192 (mp10) REVERT: B 35 TRP cc_start: 0.7610 (m-90) cc_final: 0.7383 (m-90) REVERT: B 97 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8751 (mtmt) REVERT: B 104 MET cc_start: 0.8940 (ttt) cc_final: 0.8624 (tpp) REVERT: B 108 ILE cc_start: 0.9131 (mt) cc_final: 0.8917 (mm) REVERT: G 530 MET cc_start: 0.7449 (mtp) cc_final: 0.7152 (mmm) REVERT: G 626 MET cc_start: 0.7450 (tmm) cc_final: 0.6252 (ppp) REVERT: G 648 GLU cc_start: 0.9103 (pt0) cc_final: 0.8697 (pt0) REVERT: G 650 GLN cc_start: 0.7361 (tp40) cc_final: 0.7008 (tp40) REVERT: F 104 MET cc_start: 0.8830 (ttt) cc_final: 0.8573 (tpp) REVERT: H 542 ARG cc_start: 0.6165 (ttt-90) cc_final: 0.5844 (ttp-110) REVERT: H 626 MET cc_start: 0.7236 (tmm) cc_final: 0.6724 (tmm) REVERT: J 82 LEU cc_start: 0.8742 (mm) cc_final: 0.8467 (mm) REVERT: L 12 SER cc_start: 0.7329 (t) cc_final: 0.6804 (m) REVERT: L 42 GLN cc_start: 0.8729 (mp10) cc_final: 0.8286 (mp10) REVERT: L 82 ASP cc_start: 0.8217 (m-30) cc_final: 0.7868 (m-30) REVERT: L 102 THR cc_start: 0.8506 (p) cc_final: 0.8288 (p) outliers start: 2 outliers final: 2 residues processed: 369 average time/residue: 0.3145 time to fit residues: 182.3641 Evaluate side-chains 276 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 105 optimal weight: 0.0270 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 GLN J 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20673 Z= 0.190 Angle : 0.705 11.623 28035 Z= 0.346 Chirality : 0.047 0.265 3432 Planarity : 0.004 0.047 3432 Dihedral : 7.859 59.896 4734 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2343 helix: 0.89 (0.25), residues: 420 sheet: 0.23 (0.21), residues: 591 loop : -0.51 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP G 610 HIS 0.004 0.001 HIS A 374 PHE 0.018 0.002 PHE D 76 TYR 0.028 0.002 TYR J 100E ARG 0.008 0.001 ARG G 585 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7165 (m-90) cc_final: 0.6253 (m-90) REVERT: A 256 SER cc_start: 0.8716 (p) cc_final: 0.8340 (m) REVERT: C 536 THR cc_start: 0.8565 (m) cc_final: 0.8342 (m) REVERT: C 624 ASP cc_start: 0.7834 (m-30) cc_final: 0.7608 (m-30) REVERT: C 648 GLU cc_start: 0.8966 (pt0) cc_final: 0.8724 (pt0) REVERT: C 650 GLN cc_start: 0.6765 (tp40) cc_final: 0.6341 (tp40) REVERT: D 24 THR cc_start: 0.7899 (p) cc_final: 0.7230 (p) REVERT: D 75 LEU cc_start: 0.8742 (mm) cc_final: 0.8437 (mt) REVERT: D 102 LEU cc_start: 0.7252 (mt) cc_final: 0.6945 (mt) REVERT: E 42 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8198 (mp10) REVERT: E 62 PHE cc_start: 0.7668 (m-80) cc_final: 0.7390 (m-80) REVERT: E 96 GLU cc_start: 0.8603 (pt0) cc_final: 0.8328 (pt0) REVERT: B 35 TRP cc_start: 0.7637 (m-90) cc_final: 0.7374 (m-90) REVERT: B 97 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8915 (mttt) REVERT: B 104 MET cc_start: 0.8856 (ttt) cc_final: 0.8398 (tpp) REVERT: B 108 ILE cc_start: 0.9049 (mt) cc_final: 0.8828 (mm) REVERT: G 530 MET cc_start: 0.7475 (mtp) cc_final: 0.7163 (mmm) REVERT: G 538 THR cc_start: 0.8993 (t) cc_final: 0.8764 (m) REVERT: G 621 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7145 (tm-30) REVERT: G 626 MET cc_start: 0.7548 (tmm) cc_final: 0.6702 (ppp) REVERT: G 648 GLU cc_start: 0.8961 (pt0) cc_final: 0.8176 (tm-30) REVERT: G 650 GLN cc_start: 0.6893 (tp40) cc_final: 0.6184 (tp40) REVERT: G 663 LEU cc_start: 0.6746 (mp) cc_final: 0.6279 (pp) REVERT: I 31 ARG cc_start: 0.8905 (ttm110) cc_final: 0.8653 (mtm-85) REVERT: I 102 LEU cc_start: 0.8540 (mt) cc_final: 0.8119 (mt) REVERT: I 107 THR cc_start: 0.9240 (t) cc_final: 0.9033 (m) REVERT: F 104 MET cc_start: 0.8836 (ttt) cc_final: 0.8552 (tpp) REVERT: F 427 TRP cc_start: 0.7925 (m-10) cc_final: 0.7703 (m-10) REVERT: H 624 ASP cc_start: 0.7556 (m-30) cc_final: 0.7312 (m-30) REVERT: H 626 MET cc_start: 0.7257 (tmm) cc_final: 0.6926 (tmm) REVERT: J 107 THR cc_start: 0.9104 (t) cc_final: 0.8718 (m) REVERT: L 12 SER cc_start: 0.7407 (t) cc_final: 0.6866 (m) REVERT: L 30 TYR cc_start: 0.7809 (m-80) cc_final: 0.7405 (m-80) REVERT: L 42 GLN cc_start: 0.8768 (mp10) cc_final: 0.8383 (mp10) REVERT: L 96 GLU cc_start: 0.8421 (pt0) cc_final: 0.8217 (pt0) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.3069 time to fit residues: 194.8284 Evaluate side-chains 297 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 658 GLN H 543 ASN ** H 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN J 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20673 Z= 0.312 Angle : 0.736 10.961 28035 Z= 0.365 Chirality : 0.048 0.292 3432 Planarity : 0.005 0.077 3432 Dihedral : 7.926 59.951 4734 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 0.05 % Allowed : 1.10 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2343 helix: 0.63 (0.25), residues: 438 sheet: 0.03 (0.21), residues: 594 loop : -0.66 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 610 HIS 0.005 0.001 HIS I 35A PHE 0.031 0.002 PHE D 76 TYR 0.031 0.002 TYR B 173 ARG 0.014 0.001 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 SER cc_start: 0.8736 (p) cc_final: 0.8374 (m) REVERT: C 536 THR cc_start: 0.8571 (m) cc_final: 0.8324 (m) REVERT: C 624 ASP cc_start: 0.7896 (m-30) cc_final: 0.7646 (m-30) REVERT: C 626 MET cc_start: 0.7469 (tmm) cc_final: 0.6857 (tmm) REVERT: C 648 GLU cc_start: 0.8975 (pt0) cc_final: 0.8344 (pp20) REVERT: D 75 LEU cc_start: 0.8724 (mm) cc_final: 0.8445 (mt) REVERT: E 42 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8247 (mp10) REVERT: E 46 LEU cc_start: 0.8722 (tt) cc_final: 0.8501 (tt) REVERT: E 66 GLN cc_start: 0.8229 (pp30) cc_final: 0.7963 (pp30) REVERT: B 97 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8802 (mtmt) REVERT: B 104 MET cc_start: 0.8924 (ttt) cc_final: 0.8500 (tpp) REVERT: G 530 MET cc_start: 0.7377 (mtp) cc_final: 0.7129 (mmm) REVERT: G 621 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7182 (tm-30) REVERT: G 626 MET cc_start: 0.7660 (tmm) cc_final: 0.6681 (ppp) REVERT: G 648 GLU cc_start: 0.9033 (pt0) cc_final: 0.8291 (tm-30) REVERT: G 650 GLN cc_start: 0.6840 (tp40) cc_final: 0.6309 (tp40) REVERT: I 31 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8599 (mtm-85) REVERT: I 107 THR cc_start: 0.9284 (t) cc_final: 0.9048 (m) REVERT: K 42 GLN cc_start: 0.8460 (mp10) cc_final: 0.8225 (mp10) REVERT: K 96 GLU cc_start: 0.8509 (pt0) cc_final: 0.8277 (pt0) REVERT: F 104 MET cc_start: 0.8903 (ttt) cc_final: 0.8596 (tpp) REVERT: H 626 MET cc_start: 0.7440 (tmm) cc_final: 0.7076 (tmm) REVERT: J 82 LEU cc_start: 0.8664 (mm) cc_final: 0.8442 (mm) REVERT: L 12 SER cc_start: 0.7493 (t) cc_final: 0.7003 (m) REVERT: L 30 TYR cc_start: 0.7771 (m-80) cc_final: 0.7393 (m-80) REVERT: L 42 GLN cc_start: 0.8744 (mp10) cc_final: 0.8332 (mp10) outliers start: 1 outliers final: 1 residues processed: 374 average time/residue: 0.2838 time to fit residues: 171.4915 Evaluate side-chains 289 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20673 Z= 0.216 Angle : 0.682 11.238 28035 Z= 0.337 Chirality : 0.046 0.432 3432 Planarity : 0.004 0.065 3432 Dihedral : 7.745 59.950 4734 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2343 helix: 0.84 (0.25), residues: 438 sheet: 0.18 (0.22), residues: 567 loop : -0.65 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 610 HIS 0.004 0.001 HIS J 35A PHE 0.020 0.001 PHE D 97 TYR 0.033 0.002 TYR J 100E ARG 0.020 0.001 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 SER cc_start: 0.8777 (p) cc_final: 0.8383 (m) REVERT: C 536 THR cc_start: 0.8582 (m) cc_final: 0.8343 (m) REVERT: C 624 ASP cc_start: 0.7810 (m-30) cc_final: 0.7545 (m-30) REVERT: C 626 MET cc_start: 0.7679 (tmm) cc_final: 0.7141 (tmm) REVERT: C 645 LEU cc_start: 0.8697 (mt) cc_final: 0.8432 (mt) REVERT: D 75 LEU cc_start: 0.8681 (mm) cc_final: 0.8410 (mt) REVERT: D 101 ASP cc_start: 0.7958 (p0) cc_final: 0.7350 (p0) REVERT: E 23 CYS cc_start: 0.4256 (p) cc_final: 0.3931 (p) REVERT: E 42 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8245 (mp10) REVERT: E 46 LEU cc_start: 0.8508 (tt) cc_final: 0.8236 (tt) REVERT: B 97 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8831 (mtmt) REVERT: B 104 MET cc_start: 0.8898 (ttt) cc_final: 0.8490 (tpp) REVERT: G 530 MET cc_start: 0.7392 (mtp) cc_final: 0.7171 (mmm) REVERT: G 621 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7201 (tm-30) REVERT: G 626 MET cc_start: 0.7722 (tmm) cc_final: 0.6817 (ppp) REVERT: G 648 GLU cc_start: 0.9016 (pt0) cc_final: 0.8164 (tm-30) REVERT: I 31 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8527 (mtm-85) REVERT: I 82 ILE cc_start: 0.9134 (mp) cc_final: 0.8881 (mt) REVERT: I 107 THR cc_start: 0.9264 (t) cc_final: 0.9050 (m) REVERT: K 42 GLN cc_start: 0.8438 (mp10) cc_final: 0.8174 (mp10) REVERT: K 96 GLU cc_start: 0.8488 (pt0) cc_final: 0.8266 (pt0) REVERT: F 104 MET cc_start: 0.8910 (ttt) cc_final: 0.8584 (tpp) REVERT: H 626 MET cc_start: 0.7462 (tmm) cc_final: 0.6861 (tmm) REVERT: H 632 ASP cc_start: 0.8404 (t70) cc_final: 0.8204 (t70) REVERT: J 82 LEU cc_start: 0.8680 (mm) cc_final: 0.8471 (mm) REVERT: J 86 ASP cc_start: 0.8431 (m-30) cc_final: 0.8085 (m-30) REVERT: J 87 THR cc_start: 0.9062 (m) cc_final: 0.8838 (t) REVERT: J 107 THR cc_start: 0.9271 (t) cc_final: 0.8687 (m) REVERT: L 12 SER cc_start: 0.7541 (t) cc_final: 0.7158 (m) REVERT: L 30 TYR cc_start: 0.7791 (m-80) cc_final: 0.7410 (m-80) REVERT: L 42 GLN cc_start: 0.8759 (mp10) cc_final: 0.8393 (mp10) REVERT: L 82 ASP cc_start: 0.8263 (m-30) cc_final: 0.8055 (m-30) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2918 time to fit residues: 175.5514 Evaluate side-chains 291 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 200 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20673 Z= 0.169 Angle : 0.652 15.603 28035 Z= 0.322 Chirality : 0.045 0.263 3432 Planarity : 0.004 0.052 3432 Dihedral : 7.387 59.360 4734 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2343 helix: 1.13 (0.26), residues: 435 sheet: 0.38 (0.21), residues: 612 loop : -0.53 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 610 HIS 0.008 0.001 HIS E 32 PHE 0.018 0.001 PHE D 76 TYR 0.021 0.001 TYR D 100E ARG 0.007 0.000 ARG K 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8681 (ppp) cc_final: 0.8454 (ppp) REVERT: A 104 MET cc_start: 0.8607 (ttt) cc_final: 0.8311 (tpp) REVERT: C 548 ILE cc_start: 0.3421 (tp) cc_final: 0.2643 (tt) REVERT: C 624 ASP cc_start: 0.7437 (m-30) cc_final: 0.7220 (m-30) REVERT: C 626 MET cc_start: 0.7842 (tmm) cc_final: 0.7120 (tmm) REVERT: C 649 SER cc_start: 0.8426 (p) cc_final: 0.8174 (p) REVERT: D 75 LEU cc_start: 0.8607 (mm) cc_final: 0.8352 (mt) REVERT: E 42 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8270 (mp10) REVERT: E 46 LEU cc_start: 0.8442 (tt) cc_final: 0.8092 (tt) REVERT: B 97 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8919 (mttt) REVERT: B 104 MET cc_start: 0.8857 (ttt) cc_final: 0.8394 (tpp) REVERT: B 318 TYR cc_start: 0.8646 (m-80) cc_final: 0.8397 (m-80) REVERT: G 621 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7245 (tm-30) REVERT: G 626 MET cc_start: 0.7808 (tmm) cc_final: 0.6970 (ppp) REVERT: G 648 GLU cc_start: 0.8974 (pt0) cc_final: 0.8335 (tm-30) REVERT: I 31 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8522 (mtm-85) REVERT: I 82 ILE cc_start: 0.9074 (mp) cc_final: 0.8532 (mp) REVERT: I 107 THR cc_start: 0.9248 (t) cc_final: 0.9041 (m) REVERT: K 96 GLU cc_start: 0.8428 (pt0) cc_final: 0.8214 (pt0) REVERT: F 104 MET cc_start: 0.8838 (ttt) cc_final: 0.8519 (tpp) REVERT: F 195 ASN cc_start: 0.8430 (t0) cc_final: 0.8023 (t0) REVERT: H 624 ASP cc_start: 0.7417 (m-30) cc_final: 0.7098 (m-30) REVERT: H 626 MET cc_start: 0.7542 (tmm) cc_final: 0.6919 (tmm) REVERT: J 75 LEU cc_start: 0.8692 (mm) cc_final: 0.8359 (mt) REVERT: J 82 LEU cc_start: 0.8668 (mm) cc_final: 0.8428 (mm) REVERT: J 86 ASP cc_start: 0.8422 (m-30) cc_final: 0.8107 (m-30) REVERT: J 87 THR cc_start: 0.9091 (m) cc_final: 0.8829 (t) REVERT: J 107 THR cc_start: 0.9092 (t) cc_final: 0.8719 (m) REVERT: L 12 SER cc_start: 0.7484 (t) cc_final: 0.7101 (m) REVERT: L 30 TYR cc_start: 0.7770 (m-80) cc_final: 0.7412 (m-80) REVERT: L 42 GLN cc_start: 0.8819 (mp10) cc_final: 0.8426 (mp10) REVERT: L 66 GLN cc_start: 0.8202 (pp30) cc_final: 0.7429 (tt0) REVERT: L 102 THR cc_start: 0.8417 (p) cc_final: 0.8204 (p) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2719 time to fit residues: 169.1442 Evaluate side-chains 302 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN H 607 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074356 restraints weight = 58754.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076237 restraints weight = 37864.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077558 restraints weight = 28422.661| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20673 Z= 0.489 Angle : 0.886 10.376 28035 Z= 0.441 Chirality : 0.053 0.347 3432 Planarity : 0.006 0.054 3432 Dihedral : 8.581 59.813 4734 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.66 % Favored : 93.30 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2343 helix: 0.03 (0.24), residues: 447 sheet: -0.06 (0.20), residues: 633 loop : -0.99 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP G 610 HIS 0.007 0.002 HIS I 35A PHE 0.027 0.003 PHE D 97 TYR 0.040 0.003 TYR J 100E ARG 0.008 0.001 ARG G 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.50 seconds wall clock time: 81 minutes 46.34 seconds (4906.34 seconds total)