Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 22:16:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/07_2023/8hw1_35080_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 5 Type Number sf(0) Gaussians Mg 121 5.21 5 S 55 5.16 5 C 20592 2.51 5 N 4015 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 250": "OD1" <-> "OD2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 206": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "E PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 250": "OD1" <-> "OD2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 206": "OE1" <-> "OE2" Residue "G ASP 213": "OD1" <-> "OD2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 250": "OD1" <-> "OD2" Residue "G PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G GLU 289": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H ASP 213": "OD1" <-> "OD2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 250": "OD1" <-> "OD2" Residue "H PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 285": "OE1" <-> "OE2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I ASP 106": "OD1" <-> "OD2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 206": "OE1" <-> "OE2" Residue "I ASP 213": "OD1" <-> "OD2" Residue "I ARG 216": "NH1" <-> "NH2" Residue "I PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 250": "OD1" <-> "OD2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 285": "OE1" <-> "OE2" Residue "I GLU 289": "OE1" <-> "OE2" Residue "J GLU 56": "OE1" <-> "OE2" Residue "J PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "J ARG 129": "NH1" <-> "NH2" Residue "J PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 206": "OE1" <-> "OE2" Residue "J ASP 213": "OD1" <-> "OD2" Residue "J ARG 216": "NH1" <-> "NH2" Residue "J PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 250": "OD1" <-> "OD2" Residue "J PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 285": "OE1" <-> "OE2" Residue "J GLU 289": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 116": "NH1" <-> "NH2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K ARG 129": "NH1" <-> "NH2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 206": "OE1" <-> "OE2" Residue "K ASP 213": "OD1" <-> "OD2" Residue "K ARG 216": "NH1" <-> "NH2" Residue "K PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 250": "OD1" <-> "OD2" Residue "K PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 285": "OE1" <-> "OE2" Residue "K GLU 289": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 29271 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "B" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "C" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "D" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "F" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "G" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "H" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "I" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "J" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "K" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "A" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.53, per 1000 atoms: 0.43 Number of scatterers: 29271 At special positions: 0 Unit cell: (196.62, 197.75, 67.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Mg 121 11.99 O 4488 8.00 N 4015 7.00 C 20592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=55, symmetry=0 Number of additional bonds: simple=55, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.59 Conformation dependent library (CDL) restraints added in 2.9 seconds 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 0 sheets defined 50.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 136 " --> pdb=" O MET C 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 136 " --> pdb=" O MET D 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 141 " --> pdb=" O GLY D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL E 271 " --> pdb=" O GLY E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 130 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 141 " --> pdb=" O GLY F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 221 " --> pdb=" O GLN F 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL F 271 " --> pdb=" O GLY F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 136 " --> pdb=" O MET G 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG G 221 " --> pdb=" O GLN G 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP G 238 " --> pdb=" O SER G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP G 250 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 262 No H-bonds generated for 'chain 'G' and resid 260 through 262' Processing helix chain 'G' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL G 271 " --> pdb=" O GLY G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS G 290 " --> pdb=" O LEU G 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL H 136 " --> pdb=" O MET H 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP H 238 " --> pdb=" O SER H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP H 250 " --> pdb=" O GLU H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL H 271 " --> pdb=" O GLY H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS H 290 " --> pdb=" O LEU H 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 130 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 133 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL I 136 " --> pdb=" O MET I 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 141 " --> pdb=" O GLY I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 161 through 185 removed outlier: 3.575A pdb=" N LYS I 180 " --> pdb=" O LEU I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL I 220 " --> pdb=" O ARG I 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG I 221 " --> pdb=" O GLN I 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP I 238 " --> pdb=" O SER I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP I 250 " --> pdb=" O GLU I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 262 No H-bonds generated for 'chain 'I' and resid 260 through 262' Processing helix chain 'I' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL I 271 " --> pdb=" O GLY I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 130 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 133 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 136 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL J 141 " --> pdb=" O GLY J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL J 220 " --> pdb=" O ARG J 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG J 221 " --> pdb=" O GLN J 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP J 238 " --> pdb=" O SER J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 253 removed outlier: 3.659A pdb=" N ASP J 250 " --> pdb=" O GLU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 262 No H-bonds generated for 'chain 'J' and resid 260 through 262' Processing helix chain 'J' and resid 266 through 278 removed outlier: 3.568A pdb=" N VAL J 271 " --> pdb=" O GLY J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.976A pdb=" N LEU K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 130 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL K 136 " --> pdb=" O MET K 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL K 141 " --> pdb=" O GLY K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 161 through 185 removed outlier: 3.574A pdb=" N LYS K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 239 removed outlier: 3.675A pdb=" N VAL K 220 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG K 221 " --> pdb=" O GLN K 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP K 238 " --> pdb=" O SER K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 253 removed outlier: 3.660A pdb=" N ASP K 250 " --> pdb=" O GLU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 262 No H-bonds generated for 'chain 'K' and resid 260 through 262' Processing helix chain 'K' and resid 266 through 278 removed outlier: 3.567A pdb=" N VAL K 271 " --> pdb=" O GLY K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 290 removed outlier: 3.669A pdb=" N LYS K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2574 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: 6.58 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 8287 1.35 - 1.51: 13747 1.51 - 1.67: 8304 1.67 - 1.83: 99 1.83 - 1.99: 484 Bond restraints: 30921 Sorted by residual: bond pdb=" C30 32N B 613 " pdb=" C31 32N B 613 " ideal model delta sigma weight residual 1.616 1.323 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C30 32N F 613 " pdb=" C31 32N F 613 " ideal model delta sigma weight residual 1.616 1.323 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C30 32N E 613 " pdb=" C31 32N E 613 " ideal model delta sigma weight residual 1.616 1.323 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C30 32N I 613 " pdb=" C31 32N I 613 " ideal model delta sigma weight residual 1.616 1.323 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C30 32N C 613 " pdb=" C31 32N C 613 " ideal model delta sigma weight residual 1.616 1.323 0.293 2.00e-02 2.50e+03 2.14e+02 ... (remaining 30916 not shown) Histogram of bond angle deviations from ideal: 56.89 - 79.32: 66 79.32 - 101.76: 716 101.76 - 124.19: 37945 124.19 - 146.62: 4965 146.62 - 169.06: 253 Bond angle restraints: 43945 Sorted by residual: angle pdb=" C11 32N I 613 " pdb=" C12 32N I 613 " pdb=" C13 32N I 613 " ideal model delta sigma weight residual 85.91 128.21 -42.30 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C11 32N B 613 " pdb=" C12 32N B 613 " pdb=" C13 32N B 613 " ideal model delta sigma weight residual 85.91 128.21 -42.30 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C11 32N C 613 " pdb=" C12 32N C 613 " pdb=" C13 32N C 613 " ideal model delta sigma weight residual 85.91 128.21 -42.30 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C11 32N F 613 " pdb=" C12 32N F 613 " pdb=" C13 32N F 613 " ideal model delta sigma weight residual 85.91 128.20 -42.29 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C11 32N A 613 " pdb=" C12 32N A 613 " pdb=" C13 32N A 613 " ideal model delta sigma weight residual 85.91 128.18 -42.27 3.00e+00 1.11e-01 1.99e+02 ... (remaining 43940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 11831 19.94 - 39.88: 1501 39.88 - 59.82: 693 59.82 - 79.77: 110 79.77 - 99.71: 66 Dihedral angle restraints: 14201 sinusoidal: 6743 harmonic: 7458 Sorted by residual: dihedral pdb=" CA GLY E 145 " pdb=" C GLY E 145 " pdb=" N LYS E 146 " pdb=" CA LYS E 146 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY J 145 " pdb=" C GLY J 145 " pdb=" N LYS J 146 " pdb=" CA LYS J 146 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY B 145 " pdb=" C GLY B 145 " pdb=" N LYS B 146 " pdb=" CA LYS B 146 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.987: 3707 0.987 - 1.974: 0 1.974 - 2.961: 0 2.961 - 3.949: 0 3.949 - 4.936: 11 Chirality restraints: 3718 Sorted by residual: chirality pdb=" C5 32N K 613 " pdb=" O 32N K 613 " pdb=" C4 32N K 613 " pdb=" C6 32N K 613 " both_signs ideal model delta sigma weight residual False -2.45 2.49 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" C5 32N F 613 " pdb=" O 32N F 613 " pdb=" C4 32N F 613 " pdb=" C6 32N F 613 " both_signs ideal model delta sigma weight residual False -2.45 2.49 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" C5 32N J 613 " pdb=" O 32N J 613 " pdb=" C4 32N J 613 " pdb=" C6 32N J 613 " both_signs ideal model delta sigma weight residual False -2.45 2.49 -4.93 2.00e-01 2.50e+01 6.09e+02 ... (remaining 3715 not shown) Planarity restraints: 5852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CLA H 606 " -0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA H 606 " -0.301 2.00e-02 2.50e+03 pdb=" C4A CLA H 606 " 0.284 2.00e-02 2.50e+03 pdb=" CHA CLA H 606 " 0.213 2.00e-02 2.50e+03 pdb=" NA CLA H 606 " 0.032 2.00e-02 2.50e+03 pdb="MG CLA H 606 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA C 606 " 0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA C 606 " 0.301 2.00e-02 2.50e+03 pdb=" C4A CLA C 606 " -0.284 2.00e-02 2.50e+03 pdb=" CHA CLA C 606 " -0.213 2.00e-02 2.50e+03 pdb=" NA CLA C 606 " -0.032 2.00e-02 2.50e+03 pdb="MG CLA C 606 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA F 606 " 0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA F 606 " 0.301 2.00e-02 2.50e+03 pdb=" C4A CLA F 606 " -0.283 2.00e-02 2.50e+03 pdb=" CHA CLA F 606 " -0.213 2.00e-02 2.50e+03 pdb=" NA CLA F 606 " -0.032 2.00e-02 2.50e+03 pdb="MG CLA F 606 " 0.201 2.00e-02 2.50e+03 ... (remaining 5849 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 967 2.69 - 3.24: 24927 3.24 - 3.79: 45006 3.79 - 4.35: 59152 4.35 - 4.90: 101314 Nonbonded interactions: 231366 Sorted by model distance: nonbonded pdb=" O VAL F 271 " pdb=" OG SER F 275 " model vdw 2.137 2.440 nonbonded pdb=" O VAL K 271 " pdb=" OG SER K 275 " model vdw 2.137 2.440 nonbonded pdb=" O VAL B 271 " pdb=" OG SER B 275 " model vdw 2.137 2.440 nonbonded pdb=" O VAL I 271 " pdb=" OG SER I 275 " model vdw 2.137 2.440 nonbonded pdb=" O VAL G 271 " pdb=" OG SER G 275 " model vdw 2.138 2.440 ... (remaining 231361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.280 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 60.680 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.200 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.028 0.293 30921 Z= 1.451 Angle : 2.491 42.300 43945 Z= 0.917 Chirality : 0.285 4.936 3718 Planarity : 0.029 0.208 5852 Dihedral : 22.011 99.708 9449 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer Outliers : 6.74 % 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: -2.57 (0.15), residues: 2629 helix: -0.39 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -3.23 (0.14), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 478 time to evaluate : 3.189 Fit side-chains outliers start: 143 outliers final: 43 residues processed: 557 average time/residue: 0.4337 time to fit residues: 381.4280 Evaluate side-chains 437 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 394 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2842 time to fit residues: 25.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 0.0020 chunk 68 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 0.0980 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 184 ASN B 247 ASN C 184 ASN C 247 ASN D 247 ASN E 236 GLN E 247 ASN F 247 ASN G 236 GLN H 184 ASN I 247 ASN J 247 ASN K 184 ASN K 247 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 30921 Z= 0.195 Angle : 1.010 19.100 43945 Z= 0.388 Chirality : 0.058 0.412 3718 Planarity : 0.006 0.034 5852 Dihedral : 19.655 97.082 4730 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2629 helix: 0.49 (0.14), residues: 1331 sheet: None (None), residues: 0 loop : -3.06 (0.15), residues: 1298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 419 time to evaluate : 2.715 Fit side-chains outliers start: 29 outliers final: 7 residues processed: 434 average time/residue: 0.4262 time to fit residues: 290.6685 Evaluate side-chains 376 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 369 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2679 time to fit residues: 6.8117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 30921 Z= 0.428 Angle : 1.142 18.062 43945 Z= 0.444 Chirality : 0.066 0.451 3718 Planarity : 0.008 0.062 5852 Dihedral : 19.210 87.237 4730 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2629 helix: 0.33 (0.14), residues: 1342 sheet: None (None), residues: 0 loop : -2.98 (0.15), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 421 time to evaluate : 2.641 Fit side-chains outliers start: 39 outliers final: 25 residues processed: 444 average time/residue: 0.3885 time to fit residues: 277.4773 Evaluate side-chains 414 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 389 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2601 time to fit residues: 15.4531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 255 optimal weight: 8.9990 chunk 125 optimal weight: 0.0040 chunk 228 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.003 0.025 30921 Z= 0.158 Angle : 0.892 18.110 43945 Z= 0.342 Chirality : 0.050 0.367 3718 Planarity : 0.005 0.034 5852 Dihedral : 18.613 87.817 4730 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2629 helix: 1.04 (0.14), residues: 1342 sheet: None (None), residues: 0 loop : -2.70 (0.15), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 365 time to evaluate : 2.585 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 374 average time/residue: 0.4000 time to fit residues: 238.4540 Evaluate side-chains 354 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 343 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2516 time to fit residues: 8.7072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 217 optimal weight: 0.4980 chunk 176 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 ASN F 102 GLN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 30921 Z= 0.438 Angle : 1.111 18.183 43945 Z= 0.432 Chirality : 0.064 0.450 3718 Planarity : 0.007 0.072 5852 Dihedral : 18.868 84.475 4730 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2629 helix: 0.58 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.85 (0.16), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 388 time to evaluate : 2.717 Fit side-chains outliers start: 25 outliers final: 7 residues processed: 406 average time/residue: 0.4046 time to fit residues: 262.8459 Evaluate side-chains 382 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 375 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2647 time to fit residues: 6.6406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN F 102 GLN I 127 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 30921 Z= 0.246 Angle : 0.995 18.069 43945 Z= 0.390 Chirality : 0.057 0.409 3718 Planarity : 0.006 0.069 5852 Dihedral : 18.656 87.469 4730 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2629 helix: 1.05 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.80 (0.16), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 375 time to evaluate : 2.525 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 389 average time/residue: 0.4099 time to fit residues: 252.3213 Evaluate side-chains 371 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 360 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2811 time to fit residues: 8.8483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 254 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN B 184 ASN D 184 ASN F 102 GLN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 30921 Z= 0.325 Angle : 1.040 18.120 43945 Z= 0.405 Chirality : 0.060 0.421 3718 Planarity : 0.007 0.055 5852 Dihedral : 18.724 86.063 4730 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2629 helix: 0.89 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.77 (0.16), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 371 time to evaluate : 2.494 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 389 average time/residue: 0.4090 time to fit residues: 251.7472 Evaluate side-chains 378 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 365 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2840 time to fit residues: 9.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 0.0370 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN F 102 GLN G 127 ASN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN J 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 30921 Z= 0.161 Angle : 0.892 18.098 43945 Z= 0.344 Chirality : 0.049 0.355 3718 Planarity : 0.005 0.030 5852 Dihedral : 18.377 85.655 4730 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.61 % 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: -0.59 (0.17), residues: 2629 helix: 1.46 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.64 (0.16), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 351 time to evaluate : 2.865 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 363 average time/residue: 0.4239 time to fit residues: 241.4624 Evaluate side-chains 344 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 337 time to evaluate : 2.592 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2481 time to fit residues: 6.3547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN F 102 GLN G 127 ASN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 30921 Z= 0.280 Angle : 0.985 18.143 43945 Z= 0.384 Chirality : 0.056 0.383 3718 Planarity : 0.006 0.044 5852 Dihedral : 18.453 82.810 4730 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer Outliers : 0.42 % 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: -0.69 (0.17), residues: 2629 helix: 1.31 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.59 (0.17), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 368 time to evaluate : 3.790 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 373 average time/residue: 0.4439 time to fit residues: 266.7709 Evaluate side-chains 368 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 361 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2759 time to fit residues: 6.8359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 0.0770 chunk 209 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN F 102 GLN I 127 ASN ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 30921 Z= 0.220 Angle : 0.940 18.081 43945 Z= 0.365 Chirality : 0.053 0.372 3718 Planarity : 0.006 0.038 5852 Dihedral : 18.371 83.816 4730 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer Outliers : 0.14 % 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: -0.59 (0.17), residues: 2629 helix: 1.43 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 1276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 358 time to evaluate : 2.465 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 359 average time/residue: 0.4023 time to fit residues: 229.1584 Evaluate side-chains 355 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 352 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2359 time to fit residues: 4.3088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 0.0970 chunk 215 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 38 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN F 102 GLN G 127 ASN G 184 ASN I 127 ASN ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.106762 restraints weight = 35050.014| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.64 r_work: 0.2825 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 30921 Z= 0.160 Angle : 0.877 18.369 43945 Z= 0.339 Chirality : 0.048 0.325 3718 Planarity : 0.005 0.036 5852 Dihedral : 18.096 80.558 4730 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2629 helix: 1.68 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.52 (0.17), residues: 1276 =============================================================================== Job complete usr+sys time: 5764.15 seconds wall clock time: 105 minutes 15.35 seconds (6315.35 seconds total)