Starting phenix.real_space_refine on Sun Feb 18 01:38:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/02_2024/8fis_29209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/02_2024/8fis_29209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/02_2024/8fis_29209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/02_2024/8fis_29209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/02_2024/8fis_29209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/02_2024/8fis_29209_updated.pdb" } resolution = 3.18 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= 0.005 sd= 0.053 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 134 5.16 5 C 12660 2.51 5 N 3332 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 634": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G ASP 325": "OD1" <-> "OD2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20356 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "J" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1143 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1828 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.54, per 1000 atoms: 0.57 Number of scatterers: 20356 At special positions: 0 Unit cell: (154.869, 134.292, 145.122, 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 134 16.00 O 4230 8.00 N 3332 7.00 C 12660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.08 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L1023 " - pdb=" SG CYS L1088 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA c 3 " - " MAN c 4 " " BMA p 3 " - " MAN p 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA e 3 " - " MAN e 4 " " BMA r 3 " - " MAN r 4 " " BMA w 3 " - " MAN w 5 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 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 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 T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 c 2 " - " BMA c 3 " " 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 n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 355 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 462 " " NAG D 1 " - " ASN C 197 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 618 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 339 " " NAG F 603 " - " ASN F 355 " " NAG F 604 " - " ASN F 137 " " NAG F 605 " - " ASN F 462 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 137 " " NAG G 607 " - " ASN G 462 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 295 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 392 " " NAG S 1 " - " ASN C 160 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 88 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 197 " " NAG b 1 " - " ASN F 234 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN F 295 " " NAG e 1 " - " ASN F 301 " " NAG f 1 " - " ASN F 332 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 392 " " NAG i 1 " - " ASN F 448 " " NAG j 1 " - " ASN F 160 " " NAG k 1 " - " ASN F 363 " " NAG l 1 " - " ASN F 133 " " NAG m 1 " - " ASN F 276 " " NAG n 1 " - " ASN G 197 " " NAG o 1 " - " ASN G 234 " " NAG p 1 " - " ASN G 262 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 301 " " NAG s 1 " - " ASN G 332 " " NAG t 1 " - " ASN G 386 " " NAG u 1 " - " ASN G 392 " " NAG v 1 " - " ASN G 448 " " NAG w 1 " - " ASN G 160 " " NAG x 1 " - " ASN G 363 " " NAG y 1 " - " ASN G 156 " Time building additional restraints: 12.33 Conformation dependent library (CDL) restraints added in 3.6 seconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 44 sheets defined 18.4% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.741A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.881A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.737A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 619 through 625 removed outlier: 3.935A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.847A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 662 removed outlier: 3.572A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.526A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.530A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 620 through 624 removed outlier: 3.928A pdb=" N ASP B 624 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.796A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 removed outlier: 3.648A pdb=" N THR B 639 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 641 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 644 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 651 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 652 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 655 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 656 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 660 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.670A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'E' and resid 524 through 526 No H-bonds generated for 'chain 'E' and resid 524 through 526' Processing helix chain 'E' and resid 530 through 535 removed outlier: 4.164A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 No H-bonds generated for 'chain 'E' and resid 538 through 541' Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.648A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 578 " --> pdb=" O LYS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 615 No H-bonds generated for 'chain 'E' and resid 612 through 615' Processing helix chain 'E' and resid 619 through 624 removed outlier: 3.771A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 634 removed outlier: 3.661A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 654 removed outlier: 3.542A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 660 No H-bonds generated for 'chain 'E' and resid 657 through 660' Processing helix chain 'F' and resid 58 through 64 removed outlier: 4.238A pdb=" N GLU F 62 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU F 64 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 140 through 150 No H-bonds generated for 'chain 'F' and resid 140 through 150' Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 335 through 353 removed outlier: 4.021A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 372 No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 476 through 483 removed outlier: 4.283A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 102 through 117 removed outlier: 3.673A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 335 through 351 removed outlier: 3.817A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 372 No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 387 through 389 No H-bonds generated for 'chain 'G' and resid 387 through 389' Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.515A pdb=" N ARG G 480 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 100D through 100F No H-bonds generated for 'chain 'J' and resid 100D through 100F' Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 100D through 100F No H-bonds generated for 'chain 'I' and resid 100D through 100F' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 84 through 86 No H-bonds generated for 'chain 'L' and resid 84 through 86' Processing helix chain 'L' and resid 1080 through 1082 No H-bonds generated for 'chain 'L' and resid 1080 through 1082' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.778A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.738A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.753A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.901A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 304 through 308 Processing sheet with id= J, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.528A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 423 through 425 Processing sheet with id= L, first strand: chain 'F' and resid 35 through 39 Processing sheet with id= M, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.263A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.719A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 130 through 133 Processing sheet with id= Q, first strand: chain 'F' and resid 181 through 183 Processing sheet with id= R, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.367A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ALA F 362 " --> pdb=" O PRO F 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 443 through 449 removed outlier: 3.835A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 374 through 378 removed outlier: 4.587A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 423 through 425 Processing sheet with id= V, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.638A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 35 through 39 removed outlier: 3.838A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.164A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= Z, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.249A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 130 through 133 Processing sheet with id= AB, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= AC, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.263A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ALA G 362 " --> pdb=" O PRO G 470 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 443 through 449 removed outlier: 3.659A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 423 through 425 Processing sheet with id= AF, first strand: chain 'G' and resid 303 through 312 removed outlier: 4.641A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= AH, first strand: chain 'J' and resid 107 through 109 removed outlier: 3.772A pdb=" N MET J 34 " --> pdb=" O MET J 51 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 93 through 95 removed outlier: 3.864A pdb=" N TYR J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= AK, first strand: chain 'I' and resid 89 through 94 removed outlier: 3.640A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.513A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.645A pdb=" N VAL L 5 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 57 through 59 removed outlier: 6.548A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET L 34 " --> pdb=" O GLY L 50 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR L 102 " --> pdb=" O ARG L 94 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 1009 through 1014 removed outlier: 6.012A pdb=" N GLN L1103 " --> pdb=" O VAL L1011 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA L1013 " --> pdb=" O GLN L1103 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE L1105 " --> pdb=" O ALA L1013 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'L' and resid 1019 through 1024 Processing sheet with id= AR, first strand: chain 'L' and resid 1084 through 1090 removed outlier: 3.754A pdb=" N ILE L1048 " --> pdb=" O TRP L1035 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN L1037 " --> pdb=" O LEU L1046 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU L1046 " --> pdb=" O GLN L1037 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG L1039 " --> pdb=" O PRO L1044 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1452 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: 7.07 Time building geometry restraints manager: 12.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3406 1.32 - 1.45: 5958 1.45 - 1.58: 11196 1.58 - 1.71: 2 1.71 - 1.83: 180 Bond restraints: 20742 Sorted by residual: bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" O1 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.534 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" CA SER G 199 " pdb=" CB SER G 199 " ideal model delta sigma weight residual 1.537 1.452 0.084 1.45e-02 4.76e+03 3.38e+01 ... (remaining 20737 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.61: 516 106.61 - 113.49: 12213 113.49 - 120.37: 6908 120.37 - 127.25: 8253 127.25 - 134.13: 243 Bond angle restraints: 28133 Sorted by residual: angle pdb=" N MET C 150 " pdb=" CA MET C 150 " pdb=" C MET C 150 " ideal model delta sigma weight residual 112.92 103.97 8.95 1.23e+00 6.61e-01 5.30e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 112.96 106.20 6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" C PRO G 118 " pdb=" CA PRO G 118 " pdb=" CB PRO G 118 " ideal model delta sigma weight residual 111.56 102.93 8.63 1.65e+00 3.67e-01 2.74e+01 angle pdb=" CA THR C 139 " pdb=" C THR C 139 " pdb=" O THR C 139 " ideal model delta sigma weight residual 122.01 116.96 5.05 1.05e+00 9.07e-01 2.31e+01 angle pdb=" N ASP C 141 " pdb=" CA ASP C 141 " pdb=" C ASP C 141 " ideal model delta sigma weight residual 113.97 107.90 6.07 1.28e+00 6.10e-01 2.25e+01 ... (remaining 28128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12816 22.64 - 45.28: 967 45.28 - 67.91: 223 67.91 - 90.55: 140 90.55 - 113.19: 76 Dihedral angle restraints: 14222 sinusoidal: 7470 harmonic: 6752 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual -86.00 -170.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.46 61.46 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -142.77 56.77 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 14219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3485 0.143 - 0.286: 42 0.286 - 0.429: 1 0.429 - 0.573: 0 0.573 - 0.716: 2 Chirality restraints: 3530 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN F 160 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG G 606 " pdb=" ND2 ASN G 137 " pdb=" C2 NAG G 606 " pdb=" O5 NAG G 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 3527 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 151 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.59e+00 pdb=" NE ARG C 151 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 151 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 151 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 151 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 205 " 0.044 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO C 206 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 173 " -0.013 2.00e-02 2.50e+03 1.45e-02 4.20e+00 pdb=" CG TYR F 173 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 173 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 173 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 173 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 173 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 173 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 173 " -0.001 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 437 2.67 - 3.23: 18769 3.23 - 3.78: 29291 3.78 - 4.34: 42080 4.34 - 4.90: 68370 Nonbonded interactions: 158947 Sorted by model distance: nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.110 2.440 nonbonded pdb=" O ASN G 355 " pdb=" OG SER G 397 " model vdw 2.117 2.440 nonbonded pdb=" O ASN F 478 " pdb=" OG SER F 481 " model vdw 2.179 2.440 nonbonded pdb=" O LEU B 629 " pdb=" NZ LYS B 633 " model vdw 2.205 2.520 nonbonded pdb=" OG1 THR E 606 " pdb=" O VAL F 36 " model vdw 2.213 2.440 ... (remaining 158942 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' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 703)) selection = (chain 'B' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 703)) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 32 through 185 or resid 188 through 505 or resid 601 throu \ gh 604)) selection = (chain 'F' and (resid 32 through 505 or resid 601 through 604)) selection = (chain 'G' and (resid 32 through 505 or resid 601 through 604)) } ncs_group { reference = chain 'D' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'x' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'c' selection = chain 'e' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'w' selection = chain 'y' } 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 individual isotropic 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: 3.850 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: 15.000 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 61.950 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.470 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.006 0.176 20742 Z= 0.327 Angle : 0.827 9.308 28133 Z= 0.384 Chirality : 0.055 0.716 3530 Planarity : 0.004 0.111 3407 Dihedral : 19.549 113.189 9766 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.25 % Allowed : 9.68 % Favored : 90.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2315 helix: -0.93 (0.26), residues: 377 sheet: 0.39 (0.22), residues: 597 loop : -0.98 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 69 HIS 0.011 0.001 HIS F 374 PHE 0.014 0.001 PHE G 288 TYR 0.035 0.001 TYR F 173 ARG 0.011 0.000 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 364 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 367 average time/residue: 0.3717 time to fit residues: 199.4543 Evaluate side-chains 223 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 40.0000 chunk 176 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 80 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 425 ASN E 575 GLN E 630 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 432 GLN G 33 ASN G 66 HIS G 80 ASN J 3 GLN I 73 ASN H 52AHIS L1037 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20742 Z= 0.306 Angle : 0.698 16.619 28133 Z= 0.341 Chirality : 0.048 0.400 3530 Planarity : 0.004 0.050 3407 Dihedral : 14.932 83.956 5442 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 2.56 % Allowed : 13.17 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2315 helix: -0.54 (0.25), residues: 395 sheet: 0.56 (0.22), residues: 589 loop : -1.02 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 69 HIS 0.005 0.001 HIS G 105 PHE 0.024 0.002 PHE G 288 TYR 0.025 0.001 TYR B 638 ARG 0.006 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 241 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7277 (tt0) cc_final: 0.6965 (tt0) REVERT: C 217 TYR cc_start: 0.7849 (m-80) cc_final: 0.7413 (m-80) REVERT: C 374 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6783 (p-80) REVERT: C 494 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7698 (mt) REVERT: F 475 MET cc_start: 0.7316 (mmt) cc_final: 0.6965 (mmt) REVERT: I 24 LEU cc_start: 0.8697 (tt) cc_final: 0.8475 (tp) REVERT: H 94 LYS cc_start: 0.7715 (pttt) cc_final: 0.7489 (pttm) outliers start: 52 outliers final: 22 residues processed: 280 average time/residue: 0.3208 time to fit residues: 138.6793 Evaluate side-chains 231 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 176 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 228 optimal weight: 0.0030 chunk 188 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 overall best weight: 0.9730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 543 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 114 GLN J 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20742 Z= 0.240 Angle : 0.636 11.948 28133 Z= 0.310 Chirality : 0.047 0.401 3530 Planarity : 0.003 0.050 3407 Dihedral : 12.065 72.274 5441 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 2.75 % Allowed : 15.04 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2315 helix: -0.14 (0.27), residues: 381 sheet: 0.64 (0.21), residues: 606 loop : -1.06 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 69 HIS 0.004 0.001 HIS C 374 PHE 0.016 0.002 PHE F 288 TYR 0.025 0.001 TYR B 638 ARG 0.008 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 207 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.7589 (mmm) cc_final: 0.7309 (mmm) REVERT: C 374 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.6697 (p-80) REVERT: F 374 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6501 (p-80) REVERT: F 475 MET cc_start: 0.7296 (mmt) cc_final: 0.6933 (mmt) REVERT: J 85 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: H 94 LYS cc_start: 0.7817 (pttt) cc_final: 0.7600 (pttm) outliers start: 56 outliers final: 28 residues processed: 246 average time/residue: 0.3226 time to fit residues: 123.5446 Evaluate side-chains 224 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 225 optimal weight: 0.0570 chunk 111 optimal weight: 0.9990 chunk 201 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20742 Z= 0.180 Angle : 0.600 11.598 28133 Z= 0.291 Chirality : 0.046 0.403 3530 Planarity : 0.003 0.049 3407 Dihedral : 9.838 64.739 5441 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 2.41 % Allowed : 15.58 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2315 helix: -0.02 (0.27), residues: 382 sheet: 0.74 (0.21), residues: 603 loop : -1.04 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 96 HIS 0.004 0.001 HIS C 72 PHE 0.017 0.001 PHE I 62 TYR 0.023 0.001 TYR B 638 ARG 0.004 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 374 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.6651 (p-80) REVERT: E 651 ASN cc_start: 0.5725 (m110) cc_final: 0.5200 (m-40) REVERT: F 374 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6317 (p-80) REVERT: F 475 MET cc_start: 0.7270 (mmt) cc_final: 0.6906 (mmt) REVERT: J 85 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: H 66 ARG cc_start: 0.6224 (ptt-90) cc_final: 0.5738 (ptp90) outliers start: 49 outliers final: 30 residues processed: 241 average time/residue: 0.3266 time to fit residues: 122.5966 Evaluate side-chains 225 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 0.6980 chunk 127 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN J 3 GLN H 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20742 Z= 0.225 Angle : 0.598 10.505 28133 Z= 0.292 Chirality : 0.045 0.396 3530 Planarity : 0.003 0.048 3407 Dihedral : 8.308 57.266 5441 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 3.34 % Allowed : 15.43 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2315 helix: -0.02 (0.27), residues: 392 sheet: 0.72 (0.21), residues: 590 loop : -1.06 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 69 HIS 0.004 0.001 HIS C 374 PHE 0.017 0.002 PHE G 288 TYR 0.021 0.001 TYR B 638 ARG 0.003 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 207 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.7897 (mmm) cc_final: 0.7438 (tpt) REVERT: C 217 TYR cc_start: 0.8006 (m-80) cc_final: 0.7589 (m-80) REVERT: C 374 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6637 (p-80) REVERT: F 374 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6330 (p-80) REVERT: J 85 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7570 (pm20) outliers start: 68 outliers final: 44 residues processed: 256 average time/residue: 0.3392 time to fit residues: 136.4199 Evaluate side-chains 243 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 118 optimal weight: 0.0040 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN I 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20742 Z= 0.189 Angle : 0.577 9.958 28133 Z= 0.283 Chirality : 0.044 0.391 3530 Planarity : 0.003 0.047 3407 Dihedral : 7.516 59.785 5441 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 2.46 % Allowed : 16.51 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2315 helix: 0.07 (0.27), residues: 390 sheet: 0.81 (0.21), residues: 578 loop : -1.02 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS C 72 PHE 0.015 0.001 PHE G 288 TYR 0.020 0.001 TYR B 638 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7391 (tt0) cc_final: 0.7060 (tt0) REVERT: C 150 MET cc_start: 0.7874 (mmm) cc_final: 0.7403 (tpt) REVERT: C 374 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.6629 (p-80) REVERT: F 374 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6189 (p-80) REVERT: J 82 MET cc_start: 0.7195 (mtp) cc_final: 0.6943 (mtp) REVERT: J 85 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: H 66 ARG cc_start: 0.6290 (ptt-90) cc_final: 0.5866 (mpp80) outliers start: 50 outliers final: 41 residues processed: 245 average time/residue: 0.3137 time to fit residues: 120.5207 Evaluate side-chains 244 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 224 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20742 Z= 0.269 Angle : 0.608 10.020 28133 Z= 0.298 Chirality : 0.045 0.383 3530 Planarity : 0.003 0.047 3407 Dihedral : 7.147 59.664 5441 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 3.29 % Allowed : 16.41 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2315 helix: 0.11 (0.27), residues: 383 sheet: 0.74 (0.22), residues: 586 loop : -1.07 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.004 0.001 HIS C 374 PHE 0.020 0.002 PHE G 288 TYR 0.018 0.001 TYR B 638 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 207 time to evaluate : 2.220 Fit side-chains revert: symmetry clash REVERT: C 374 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.6625 (p-80) REVERT: F 374 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.6365 (p-80) REVERT: J 82 MET cc_start: 0.7295 (mtp) cc_final: 0.6929 (mtp) REVERT: J 85 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7576 (pm20) outliers start: 67 outliers final: 50 residues processed: 258 average time/residue: 0.3012 time to fit residues: 122.1950 Evaluate side-chains 252 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20742 Z= 0.166 Angle : 0.564 10.349 28133 Z= 0.278 Chirality : 0.043 0.382 3530 Planarity : 0.003 0.046 3407 Dihedral : 6.828 59.303 5441 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 2.75 % Allowed : 17.10 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2315 helix: 0.40 (0.28), residues: 367 sheet: 0.86 (0.22), residues: 578 loop : -1.01 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 36 HIS 0.007 0.001 HIS H 52A PHE 0.018 0.001 PHE I 17 TYR 0.020 0.001 TYR B 638 ARG 0.004 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 374 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.6481 (p-80) REVERT: F 374 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.6176 (p-80) REVERT: J 85 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: H 66 ARG cc_start: 0.6313 (ptt-90) cc_final: 0.5895 (mpp80) outliers start: 56 outliers final: 42 residues processed: 249 average time/residue: 0.3034 time to fit residues: 119.9881 Evaluate side-chains 242 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 0.3980 chunk 215 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20742 Z= 0.190 Angle : 0.573 10.625 28133 Z= 0.282 Chirality : 0.043 0.375 3530 Planarity : 0.003 0.046 3407 Dihedral : 6.726 59.984 5441 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 2.60 % Allowed : 17.05 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2315 helix: 0.38 (0.28), residues: 367 sheet: 0.88 (0.22), residues: 578 loop : -1.00 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.011 0.001 HIS H 52A PHE 0.018 0.001 PHE I 17 TYR 0.019 0.001 TYR B 638 ARG 0.005 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.6499 (p-80) REVERT: F 374 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.6199 (p-80) REVERT: J 82 MET cc_start: 0.7239 (mtp) cc_final: 0.6948 (mtp) REVERT: J 85 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7582 (pm20) outliers start: 53 outliers final: 48 residues processed: 240 average time/residue: 0.3013 time to fit residues: 113.8356 Evaluate side-chains 245 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 194 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 153 optimal weight: 0.3980 chunk 232 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 0.0370 chunk 113 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 100CASN J 100EASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20742 Z= 0.156 Angle : 0.554 10.528 28133 Z= 0.273 Chirality : 0.043 0.371 3530 Planarity : 0.003 0.046 3407 Dihedral : 6.540 59.366 5441 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 2.51 % Allowed : 17.20 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2315 helix: 0.47 (0.28), residues: 366 sheet: 0.83 (0.21), residues: 611 loop : -0.96 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.009 0.001 HIS H 52A PHE 0.018 0.001 PHE I 17 TYR 0.020 0.001 TYR B 638 ARG 0.004 0.000 ARG A 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.6714 (p-80) REVERT: F 374 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6085 (p-80) REVERT: J 82 MET cc_start: 0.7156 (mtp) cc_final: 0.6820 (mtp) REVERT: J 85 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: H 82 MET cc_start: 0.3978 (mmt) cc_final: 0.3736 (mmt) outliers start: 51 outliers final: 43 residues processed: 240 average time/residue: 0.3050 time to fit residues: 116.6505 Evaluate side-chains 244 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 190 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN J 3 GLN J 100CASN J 100EASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081278 restraints weight = 38051.363| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.91 r_work: 0.2994 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20742 Z= 0.214 Angle : 0.573 9.946 28133 Z= 0.283 Chirality : 0.043 0.367 3530 Planarity : 0.003 0.046 3407 Dihedral : 6.542 59.291 5441 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2315 helix: 0.41 (0.28), residues: 367 sheet: 0.75 (0.21), residues: 617 loop : -0.97 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.007 0.001 HIS H 52A PHE 0.018 0.002 PHE I 17 TYR 0.019 0.001 TYR B 638 ARG 0.006 0.000 ARG C 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4150.75 seconds wall clock time: 77 minutes 12.66 seconds (4632.66 seconds total)