Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 21:18:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/05_2023/6crq_7568.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/05_2023/6crq_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_7568/05_2023/6crq_7568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/05_2023/6crq_7568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/05_2023/6crq_7568.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crq_7568/05_2023/6crq_7568.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4953/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 10.34, 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: 9.17 Conformation dependent library (CDL) restraints added in 2.9 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: 1.59 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: 7.84 Time building geometry restraints manager: 9.79 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 - 17.77: 10983 17.77 - 35.54: 373 35.54 - 53.31: 125 53.31 - 71.08: 46 71.08 - 88.85: 17 Dihedral angle restraints: 11544 sinusoidal: 4692 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 11541 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: 4.000 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: 0.010 Extract box with map and model: 7.910 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 53.670 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.880 ------------------------------------------------------------------------------- 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 : 11.524 88.852 7020 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 % 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 *********************** 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 : 2.409 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 outliers start: 22 outliers final: 4 residues processed: 746 average time/residue: 0.3677 time to fit residues: 400.1752 Evaluate side-chains 349 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1776 time to fit residues: 4.4616 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20673 Z= 0.221 Angle : 0.796 15.470 28035 Z= 0.398 Chirality : 0.050 0.473 3432 Planarity : 0.005 0.071 3432 Dihedral : 5.315 30.328 2559 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.34 % 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: 1.49 (0.17), residues: 2343 helix: 0.97 (0.24), residues: 435 sheet: 0.78 (0.19), residues: 630 loop : 1.34 (0.18), residues: 1278 *********************** 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 510 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 503 time to evaluate : 2.575 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 outliers start: 7 outliers final: 2 residues processed: 509 average time/residue: 0.3178 time to fit residues: 246.7851 Evaluate side-chains 320 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 318 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1955 time to fit residues: 3.7306 ------------------------------------------------------------------------------- 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: 6.9990 chunk 179 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 232 optimal weight: 0.1980 chunk 192 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 chunk 172 optimal weight: 7.9990 overall best weight: 2.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 GLN H 625 ASN J 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20673 Z= 0.242 Angle : 0.753 15.055 28035 Z= 0.369 Chirality : 0.049 0.482 3432 Planarity : 0.004 0.054 3432 Dihedral : 5.137 29.726 2559 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.24 % 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: 1.17 (0.17), residues: 2343 helix: 1.23 (0.25), residues: 417 sheet: 0.64 (0.19), residues: 684 loop : 0.89 (0.18), residues: 1242 *********************** 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 424 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 419 time to evaluate : 2.431 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 outliers start: 5 outliers final: 3 residues processed: 423 average time/residue: 0.3074 time to fit residues: 202.5671 Evaluate side-chains 296 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 2.145 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2063 time to fit residues: 4.2507 ------------------------------------------------------------------------------- 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: 0.4980 chunk 162 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 287 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN B 170 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.005 0.079 20673 Z= 0.307 Angle : 0.779 13.800 28035 Z= 0.381 Chirality : 0.051 0.436 3432 Planarity : 0.005 0.056 3432 Dihedral : 5.322 30.637 2559 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.05 % 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: 0.61 (0.17), residues: 2343 helix: 1.02 (0.25), residues: 414 sheet: 0.54 (0.20), residues: 654 loop : 0.25 (0.17), residues: 1275 *********************** 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 394 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 2.380 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 outliers start: 1 outliers final: 1 residues processed: 394 average time/residue: 0.3097 time to fit residues: 191.0838 Evaluate side-chains 284 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2379 time to fit residues: 3.6869 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS I 6 GLN I 39 GLN I 43 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 20673 Z= 0.353 Angle : 0.789 13.607 28035 Z= 0.386 Chirality : 0.051 0.492 3432 Planarity : 0.005 0.045 3432 Dihedral : 5.486 31.182 2559 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.10 % 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: 0.14 (0.17), residues: 2343 helix: 0.85 (0.25), residues: 405 sheet: 0.36 (0.21), residues: 603 loop : -0.20 (0.16), residues: 1335 *********************** 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 392 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 2.454 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 outliers start: 2 outliers final: 1 residues processed: 392 average time/residue: 0.3162 time to fit residues: 193.2124 Evaluate side-chains 285 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2112 time to fit residues: 3.3902 ------------------------------------------------------------------------------- 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: 6.9990 chunk 206 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 229 optimal weight: 0.4980 chunk 190 optimal weight: 0.0060 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN C 650 GLN D 6 GLN B 203 GLN I 39 GLN F 99 ASN H 651 ASN J 1 GLN J 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20673 Z= 0.171 Angle : 0.682 12.808 28035 Z= 0.334 Chirality : 0.048 0.550 3432 Planarity : 0.004 0.044 3432 Dihedral : 5.062 29.717 2559 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.19 % 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: 0.43 (0.17), residues: 2343 helix: 1.28 (0.26), residues: 402 sheet: 0.70 (0.20), residues: 612 loop : -0.17 (0.17), residues: 1329 *********************** 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 403 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 399 time to evaluate : 2.196 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 outliers start: 4 outliers final: 0 residues processed: 401 average time/residue: 0.3045 time to fit residues: 192.6565 Evaluate side-chains 293 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2097 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN H 653 GLN J 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.082 20673 Z= 0.451 Angle : 0.837 11.881 28035 Z= 0.411 Chirality : 0.053 0.543 3432 Planarity : 0.005 0.045 3432 Dihedral : 5.547 32.147 2559 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.68 % Favored : 94.28 % Rotamer Outliers : 0.00 % 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: -0.37 (0.17), residues: 2343 helix: 0.48 (0.24), residues: 405 sheet: 0.15 (0.21), residues: 591 loop : -0.62 (0.16), residues: 1347 *********************** 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 354 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2874 time to fit residues: 163.1370 Evaluate side-chains 270 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8324 ------------------------------------------------------------------------------- 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: 0.9980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 650 GLN G 651 ASN G 653 GLN I 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20673 Z= 0.198 Angle : 0.696 12.399 28035 Z= 0.341 Chirality : 0.049 0.509 3432 Planarity : 0.004 0.044 3432 Dihedral : 5.203 31.205 2559 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer Outliers : 0.00 % 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: -0.14 (0.17), residues: 2343 helix: 0.86 (0.25), residues: 402 sheet: 0.30 (0.20), residues: 639 loop : -0.56 (0.17), residues: 1302 *********************** 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 383 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.372 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 outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2700 time to fit residues: 165.7151 Evaluate side-chains 294 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3580 ------------------------------------------------------------------------------- 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: 7.9990 chunk 199 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 625 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 20673 Z= 0.293 Angle : 0.744 12.148 28035 Z= 0.364 Chirality : 0.049 0.499 3432 Planarity : 0.005 0.068 3432 Dihedral : 5.381 31.906 2559 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.15 % Rotamer Outliers : 0.00 % 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: -0.32 (0.17), residues: 2343 helix: 0.72 (0.25), residues: 417 sheet: 0.17 (0.20), residues: 645 loop : -0.69 (0.17), residues: 1281 *********************** 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 356 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.519 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 outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2853 time to fit residues: 163.6410 Evaluate side-chains 274 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0286 ------------------------------------------------------------------------------- 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: 0.8980 chunk 106 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN H 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6353 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: