Starting phenix.real_space_refine on Tue Feb 20 23:43:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_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_35080/02_2024/8hw1_35080_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw1_35080/02_2024/8hw1_35080_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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-dev-5238/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: 14.16, per 1000 atoms: 0.48 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: 12.10 Conformation dependent library (CDL) restraints added in 4.0 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: 4.53 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: 7.02 Time building geometry restraints manager: 12.72 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 - 21.68: 12111 21.68 - 43.36: 1485 43.36 - 65.04: 616 65.04 - 86.72: 121 86.72 - 108.40: 66 Dihedral angle restraints: 14399 sinusoidal: 6941 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 14396 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.330 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 70.330 Find NCS groups from input model: 1.740 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.140 ------------------------------------------------------------------------------- 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 : 22.713 108.398 9647 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 % Allowed : 7.77 % Favored : 85.49 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 69 HIS 0.009 0.003 HIS K 193 PHE 0.022 0.003 PHE I 230 TYR 0.008 0.001 TYR K 68 ARG 0.013 0.002 ARG K 116 *********************** 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 : 2.771 Fit side-chains REVERT: A 57 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6789 (tp30) REVERT: A 115 SER cc_start: 0.8882 (t) cc_final: 0.8646 (m) REVERT: A 132 MET cc_start: 0.8638 (mtm) cc_final: 0.8226 (mtp) REVERT: B 115 SER cc_start: 0.8821 (t) cc_final: 0.8593 (m) REVERT: B 132 MET cc_start: 0.8667 (mtm) cc_final: 0.8258 (mtp) REVERT: B 190 GLU cc_start: 0.8035 (tt0) cc_final: 0.7816 (tt0) REVERT: B 290 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6846 (ttmt) REVERT: C 200 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (t0) REVERT: C 290 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6951 (ttpt) REVERT: D 54 MET cc_start: 0.8292 (mtp) cc_final: 0.8024 (mtp) REVERT: D 204 LEU cc_start: 0.8701 (mt) cc_final: 0.8426 (mp) REVERT: E 59 ASP cc_start: 0.8286 (p0) cc_final: 0.8080 (p0) REVERT: E 180 LYS cc_start: 0.8673 (tptt) cc_final: 0.8300 (tptt) REVERT: E 200 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7990 (t0) REVERT: E 227 MET cc_start: 0.9042 (mtt) cc_final: 0.8768 (mtp) REVERT: F 115 SER cc_start: 0.8836 (t) cc_final: 0.8596 (m) REVERT: F 180 LYS cc_start: 0.8883 (tptt) cc_final: 0.8679 (tptm) REVERT: F 246 GLU cc_start: 0.6896 (mp0) cc_final: 0.6535 (mp0) REVERT: G 132 MET cc_start: 0.8651 (mtm) cc_final: 0.8423 (mtm) REVERT: G 180 LYS cc_start: 0.8675 (tptt) cc_final: 0.7996 (tptm) REVERT: H 132 MET cc_start: 0.8654 (mtm) cc_final: 0.8357 (mtp) REVERT: H 180 LYS cc_start: 0.8796 (tptt) cc_final: 0.8313 (tptm) REVERT: I 102 GLN cc_start: 0.8896 (mt0) cc_final: 0.8444 (mt0) REVERT: I 115 SER cc_start: 0.8850 (t) cc_final: 0.8621 (m) REVERT: I 132 MET cc_start: 0.8622 (mtm) cc_final: 0.8417 (mtp) REVERT: I 180 LYS cc_start: 0.8568 (tptt) cc_final: 0.7773 (tptm) REVERT: I 184 ASN cc_start: 0.7911 (m-40) cc_final: 0.7665 (m110) REVERT: I 190 GLU cc_start: 0.8155 (tt0) cc_final: 0.7778 (tt0) REVERT: I 200 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8345 (t0) REVERT: J 132 MET cc_start: 0.8588 (mtm) cc_final: 0.8217 (mtp) REVERT: J 200 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: K 117 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (mt) REVERT: K 227 MET cc_start: 0.8986 (mtt) cc_final: 0.8727 (mtm) outliers start: 143 outliers final: 43 residues processed: 557 average time/residue: 0.4494 time to fit residues: 395.8295 Evaluate side-chains 448 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 397 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 200 ASP Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 257 GLU 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: 0.0030 chunk 68 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 chunk 154 optimal weight: 5.9990 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8192 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30921 Z= 0.193 Angle : 1.006 19.127 43945 Z= 0.387 Chirality : 0.060 0.412 3718 Planarity : 0.006 0.034 5852 Dihedral : 20.983 103.347 5043 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.01 % Allowed : 13.09 % Favored : 83.89 % 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: -1.71 (0.16), residues: 2629 helix: 0.49 (0.14), residues: 1331 sheet: None (None), residues: 0 loop : -3.06 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 100 HIS 0.008 0.002 HIS F 171 PHE 0.020 0.001 PHE A 230 TYR 0.015 0.002 TYR E 112 ARG 0.003 0.001 ARG D 89 *********************** 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 482 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 418 time to evaluate : 2.605 Fit side-chains REVERT: A 57 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6670 (tp30) REVERT: A 132 MET cc_start: 0.8567 (mtm) cc_final: 0.8159 (mtp) REVERT: A 183 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 213 ASP cc_start: 0.8551 (p0) cc_final: 0.8310 (p0) REVERT: B 57 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6543 (tp30) REVERT: B 115 SER cc_start: 0.8785 (t) cc_final: 0.8523 (m) REVERT: C 57 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: C 200 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7968 (t0) REVERT: D 54 MET cc_start: 0.8205 (mtp) cc_final: 0.7937 (mtp) REVERT: D 57 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: D 59 ASP cc_start: 0.8167 (p0) cc_final: 0.7942 (p0) REVERT: D 180 LYS cc_start: 0.8684 (tptt) cc_final: 0.8263 (tptm) REVERT: D 204 LEU cc_start: 0.8681 (mt) cc_final: 0.8388 (mp) REVERT: D 210 LEU cc_start: 0.8739 (mp) cc_final: 0.8477 (mt) REVERT: D 213 ASP cc_start: 0.8523 (p0) cc_final: 0.8316 (p0) REVERT: E 57 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: E 88 ASP cc_start: 0.8873 (t0) cc_final: 0.8642 (t70) REVERT: E 200 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7932 (t0) REVERT: E 213 ASP cc_start: 0.8510 (p0) cc_final: 0.8289 (p0) REVERT: F 57 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6535 (tp30) REVERT: F 115 SER cc_start: 0.8841 (t) cc_final: 0.8573 (m) REVERT: F 130 LEU cc_start: 0.8235 (mp) cc_final: 0.8013 (mp) REVERT: G 57 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: G 180 LYS cc_start: 0.8634 (tptt) cc_final: 0.8124 (tptm) REVERT: H 57 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: H 180 LYS cc_start: 0.8760 (tptt) cc_final: 0.8320 (tptm) REVERT: I 57 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: I 184 ASN cc_start: 0.7867 (m-40) cc_final: 0.7608 (m110) REVERT: I 200 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8202 (t0) REVERT: I 213 ASP cc_start: 0.8470 (p0) cc_final: 0.8267 (p0) REVERT: J 57 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: J 132 MET cc_start: 0.8574 (mtm) cc_final: 0.8268 (mtp) REVERT: K 57 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6987 (mm-30) outliers start: 64 outliers final: 11 residues processed: 461 average time/residue: 0.4198 time to fit residues: 304.7103 Evaluate side-chains 403 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 378 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain K residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.0000 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN K 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 30921 Z= 0.565 Angle : 1.235 18.107 43945 Z= 0.484 Chirality : 0.071 0.501 3718 Planarity : 0.008 0.079 5852 Dihedral : 20.530 106.285 4980 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.54 % Allowed : 16.91 % Favored : 80.55 % 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: -2.11 (0.15), residues: 2629 helix: -0.02 (0.13), residues: 1342 sheet: None (None), residues: 0 loop : -3.07 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 69 HIS 0.012 0.003 HIS I 80 PHE 0.032 0.003 PHE C 230 TYR 0.021 0.003 TYR F 68 ARG 0.012 0.002 ARG G 221 *********************** 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 464 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 410 time to evaluate : 2.693 Fit side-chains REVERT: A 132 MET cc_start: 0.8677 (mtm) cc_final: 0.8121 (mtp) REVERT: B 115 SER cc_start: 0.8801 (t) cc_final: 0.8504 (m) REVERT: C 200 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7986 (t0) REVERT: C 290 LYS cc_start: 0.7426 (mtpp) cc_final: 0.7158 (ttpt) REVERT: D 54 MET cc_start: 0.8241 (mtp) cc_final: 0.7989 (mtp) REVERT: D 213 ASP cc_start: 0.8758 (p0) cc_final: 0.8514 (p0) REVERT: E 117 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8240 (tt) REVERT: E 180 LYS cc_start: 0.8591 (tptt) cc_final: 0.8125 (tptm) REVERT: E 200 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7817 (t0) REVERT: E 290 LYS cc_start: 0.7585 (mtpp) cc_final: 0.7320 (ttmt) REVERT: F 57 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: F 115 SER cc_start: 0.9051 (t) cc_final: 0.8789 (m) REVERT: G 180 LYS cc_start: 0.8704 (tptt) cc_final: 0.8104 (tptm) REVERT: H 180 LYS cc_start: 0.8705 (tptt) cc_final: 0.8295 (tptm) REVERT: I 180 LYS cc_start: 0.8558 (tptt) cc_final: 0.8107 (tptm) REVERT: I 246 GLU cc_start: 0.6885 (mp0) cc_final: 0.6517 (mp0) REVERT: I 250 ASP cc_start: 0.7366 (m-30) cc_final: 0.7090 (m-30) REVERT: J 200 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8220 (m-30) outliers start: 54 outliers final: 30 residues processed: 441 average time/residue: 0.3847 time to fit residues: 272.8506 Evaluate side-chains 431 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 396 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 200 ASP Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain K residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 228 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.2250 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= 0.176 Angle : 0.923 18.087 43945 Z= 0.354 Chirality : 0.053 0.392 3718 Planarity : 0.006 0.034 5852 Dihedral : 19.352 102.317 4948 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.46 % Allowed : 18.98 % Favored : 79.56 % 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: -1.18 (0.16), residues: 2629 helix: 0.86 (0.14), residues: 1342 sheet: None (None), residues: 0 loop : -2.75 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 100 HIS 0.006 0.001 HIS F 171 PHE 0.017 0.001 PHE A 230 TYR 0.011 0.001 TYR E 112 ARG 0.004 0.000 ARG I 89 *********************** 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 408 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 377 time to evaluate : 2.514 Fit side-chains REVERT: A 132 MET cc_start: 0.8443 (mtm) cc_final: 0.8133 (mtp) REVERT: B 115 SER cc_start: 0.8589 (t) cc_final: 0.8369 (m) REVERT: B 213 ASP cc_start: 0.8608 (p0) cc_final: 0.8387 (p0) REVERT: C 200 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7824 (t0) REVERT: C 290 LYS cc_start: 0.7300 (mtpp) cc_final: 0.7086 (ttpt) REVERT: D 54 MET cc_start: 0.8186 (mtp) cc_final: 0.7950 (mtp) REVERT: D 180 LYS cc_start: 0.8764 (tptt) cc_final: 0.8428 (tptm) REVERT: D 213 ASP cc_start: 0.8633 (p0) cc_final: 0.8405 (p0) REVERT: E 180 LYS cc_start: 0.8596 (tptt) cc_final: 0.8244 (tptm) REVERT: E 200 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7767 (t0) REVERT: F 213 ASP cc_start: 0.8630 (p0) cc_final: 0.8407 (p0) REVERT: G 180 LYS cc_start: 0.8724 (tptt) cc_final: 0.8225 (tptm) REVERT: H 180 LYS cc_start: 0.8710 (tptt) cc_final: 0.8299 (tptm) REVERT: H 206 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7793 (mt-10) REVERT: I 180 LYS cc_start: 0.8635 (tptt) cc_final: 0.8150 (tptm) REVERT: K 190 GLU cc_start: 0.8011 (tt0) cc_final: 0.7801 (tt0) outliers start: 31 outliers final: 14 residues processed: 398 average time/residue: 0.3966 time to fit residues: 252.0413 Evaluate side-chains 381 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 365 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 217 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2264 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= 0.335 Angle : 1.038 18.126 43945 Z= 0.401 Chirality : 0.060 0.418 3718 Planarity : 0.007 0.056 5852 Dihedral : 19.383 104.150 4935 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 2.68 % Allowed : 19.97 % Favored : 77.34 % 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: -1.30 (0.16), residues: 2629 helix: 0.77 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.85 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 150 HIS 0.007 0.002 HIS J 171 PHE 0.022 0.002 PHE B 230 TYR 0.012 0.002 TYR G 68 ARG 0.007 0.001 ARG D 221 *********************** 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 460 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 403 time to evaluate : 2.889 Fit side-chains REVERT: B 115 SER cc_start: 0.8695 (t) cc_final: 0.8452 (m) REVERT: C 200 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7913 (t0) REVERT: D 54 MET cc_start: 0.8219 (mtp) cc_final: 0.7995 (mtp) REVERT: D 180 LYS cc_start: 0.8793 (tptt) cc_final: 0.8414 (tptm) REVERT: D 213 ASP cc_start: 0.8750 (p0) cc_final: 0.8511 (p0) REVERT: E 180 LYS cc_start: 0.8689 (tptt) cc_final: 0.8254 (tptm) REVERT: F 213 ASP cc_start: 0.8628 (p0) cc_final: 0.8391 (p0) REVERT: G 180 LYS cc_start: 0.8762 (tptt) cc_final: 0.8230 (tptm) REVERT: H 180 LYS cc_start: 0.8747 (tptt) cc_final: 0.8323 (tptm) REVERT: H 206 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7757 (mt-10) REVERT: I 180 LYS cc_start: 0.8615 (tptt) cc_final: 0.8335 (tptt) REVERT: I 246 GLU cc_start: 0.6795 (mp0) cc_final: 0.6417 (mp0) REVERT: I 250 ASP cc_start: 0.7291 (m-30) cc_final: 0.7005 (m-30) outliers start: 57 outliers final: 35 residues processed: 441 average time/residue: 0.3873 time to fit residues: 274.8714 Evaluate side-chains 418 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 382 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain K residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 134 optimal weight: 0.0020 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN I 127 ASN ** 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: 0.8267 moved from start: 0.2382 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= 0.284 Angle : 1.018 18.093 43945 Z= 0.398 Chirality : 0.059 0.414 3718 Planarity : 0.007 0.071 5852 Dihedral : 19.219 102.960 4930 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.40 % Allowed : 21.15 % Favored : 76.45 % 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: -1.11 (0.16), residues: 2629 helix: 0.98 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.83 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 100 HIS 0.006 0.001 HIS H 171 PHE 0.020 0.002 PHE A 230 TYR 0.012 0.002 TYR E 112 ARG 0.006 0.001 ARG G 221 *********************** 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 437 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 386 time to evaluate : 2.586 Fit side-chains REVERT: B 115 SER cc_start: 0.8662 (t) cc_final: 0.8442 (m) REVERT: C 200 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7902 (t0) REVERT: D 54 MET cc_start: 0.8212 (mtp) cc_final: 0.7990 (mtp) REVERT: D 180 LYS cc_start: 0.8797 (tptt) cc_final: 0.8432 (tptm) REVERT: D 213 ASP cc_start: 0.8749 (p0) cc_final: 0.8512 (p0) REVERT: E 180 LYS cc_start: 0.8642 (tptt) cc_final: 0.8202 (tptm) REVERT: F 213 ASP cc_start: 0.8637 (p0) cc_final: 0.8400 (p0) REVERT: G 59 ASP cc_start: 0.8127 (p0) cc_final: 0.7887 (p0) REVERT: G 180 LYS cc_start: 0.8746 (tptt) cc_final: 0.8191 (tptm) REVERT: H 180 LYS cc_start: 0.8764 (tptt) cc_final: 0.8346 (tptm) REVERT: H 206 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7730 (mt-10) REVERT: I 180 LYS cc_start: 0.8391 (tptt) cc_final: 0.8142 (tptm) REVERT: I 246 GLU cc_start: 0.6776 (mp0) cc_final: 0.6398 (mp0) REVERT: I 250 ASP cc_start: 0.7329 (m-30) cc_final: 0.7055 (m-30) REVERT: J 180 LYS cc_start: 0.8705 (tptt) cc_final: 0.8429 (tptt) outliers start: 51 outliers final: 37 residues processed: 417 average time/residue: 0.3929 time to fit residues: 259.9821 Evaluate side-chains 413 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 375 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN I 127 ASN ** 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: 0.8264 moved from start: 0.2493 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= 0.270 Angle : 0.995 18.116 43945 Z= 0.386 Chirality : 0.057 0.407 3718 Planarity : 0.006 0.048 5852 Dihedral : 19.157 102.342 4930 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 2.59 % Allowed : 21.20 % Favored : 76.21 % 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: -0.99 (0.17), residues: 2629 helix: 1.07 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.75 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 149 HIS 0.006 0.001 HIS J 171 PHE 0.019 0.002 PHE A 230 TYR 0.012 0.002 TYR E 112 ARG 0.006 0.001 ARG H 89 *********************** 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 438 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 383 time to evaluate : 2.705 Fit side-chains REVERT: B 115 SER cc_start: 0.8660 (t) cc_final: 0.8449 (m) REVERT: B 213 ASP cc_start: 0.8708 (p0) cc_final: 0.8500 (p0) REVERT: B 290 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7355 (ttmt) REVERT: C 200 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7904 (t0) REVERT: D 54 MET cc_start: 0.8256 (mtp) cc_final: 0.8036 (mtp) REVERT: D 180 LYS cc_start: 0.8796 (tptt) cc_final: 0.8418 (tptm) REVERT: D 213 ASP cc_start: 0.8763 (p0) cc_final: 0.8526 (p0) REVERT: E 142 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 180 LYS cc_start: 0.8649 (tptt) cc_final: 0.8229 (tptm) REVERT: E 206 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: E 221 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8327 (mtt-85) REVERT: F 213 ASP cc_start: 0.8660 (p0) cc_final: 0.8408 (p0) REVERT: G 59 ASP cc_start: 0.8235 (p0) cc_final: 0.8006 (p0) REVERT: G 180 LYS cc_start: 0.8760 (tptt) cc_final: 0.8209 (tptm) REVERT: H 180 LYS cc_start: 0.8763 (tptt) cc_final: 0.8334 (tptm) REVERT: H 206 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7720 (mt-10) REVERT: I 180 LYS cc_start: 0.8414 (tptt) cc_final: 0.8106 (tptm) REVERT: J 180 LYS cc_start: 0.8815 (tptt) cc_final: 0.8555 (tptt) outliers start: 55 outliers final: 39 residues processed: 419 average time/residue: 0.4038 time to fit residues: 268.9853 Evaluate side-chains 418 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 376 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 223 CYS Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 0.4980 chunk 125 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.7280 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30921 Z= 0.201 Angle : 0.933 18.112 43945 Z= 0.359 Chirality : 0.053 0.377 3718 Planarity : 0.006 0.036 5852 Dihedral : 18.983 101.120 4930 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.88 % Allowed : 22.04 % Favored : 76.07 % 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: -0.62 (0.17), residues: 2629 helix: 1.41 (0.14), residues: 1342 sheet: None (None), residues: 0 loop : -2.58 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 149 HIS 0.005 0.001 HIS F 171 PHE 0.017 0.001 PHE A 230 TYR 0.011 0.001 TYR E 112 ARG 0.003 0.000 ARG H 288 *********************** 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 403 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 363 time to evaluate : 2.634 Fit side-chains REVERT: B 213 ASP cc_start: 0.8698 (p0) cc_final: 0.8482 (p0) REVERT: B 290 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7342 (ttmt) REVERT: C 200 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7887 (t0) REVERT: D 54 MET cc_start: 0.8262 (mtp) cc_final: 0.8047 (mtp) REVERT: D 180 LYS cc_start: 0.8812 (tptt) cc_final: 0.8418 (tptm) REVERT: D 213 ASP cc_start: 0.8732 (p0) cc_final: 0.8504 (p0) REVERT: E 180 LYS cc_start: 0.8641 (tptt) cc_final: 0.8291 (tptm) REVERT: E 206 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: E 221 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8494 (mtt180) REVERT: F 213 ASP cc_start: 0.8641 (p0) cc_final: 0.8399 (p0) REVERT: F 228 LEU cc_start: 0.8508 (pt) cc_final: 0.8204 (mt) REVERT: G 59 ASP cc_start: 0.8182 (p0) cc_final: 0.7977 (p0) REVERT: G 180 LYS cc_start: 0.8752 (tptt) cc_final: 0.8213 (tptm) REVERT: H 180 LYS cc_start: 0.8780 (tptt) cc_final: 0.8332 (tptm) REVERT: H 206 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7779 (mt-10) REVERT: I 180 LYS cc_start: 0.8435 (tptt) cc_final: 0.8135 (tptm) REVERT: I 246 GLU cc_start: 0.6788 (mp0) cc_final: 0.6412 (mp0) REVERT: I 250 ASP cc_start: 0.7299 (m-30) cc_final: 0.7000 (m-30) REVERT: K 263 TYR cc_start: 0.8745 (m-80) cc_final: 0.8501 (m-80) outliers start: 40 outliers final: 30 residues processed: 393 average time/residue: 0.4159 time to fit residues: 257.8108 Evaluate side-chains 387 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 354 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain K residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN D 247 ASN E 111 ASN F 102 GLN G 184 ASN I 127 ASN J 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30921 Z= 0.340 Angle : 1.041 18.169 43945 Z= 0.406 Chirality : 0.060 0.410 3718 Planarity : 0.007 0.047 5852 Dihedral : 19.169 102.343 4930 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 2.12 % Allowed : 21.95 % Favored : 75.93 % 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: -0.96 (0.17), residues: 2629 helix: 1.06 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -2.69 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 149 HIS 0.006 0.001 HIS G 171 PHE 0.022 0.002 PHE I 230 TYR 0.012 0.002 TYR K 112 ARG 0.008 0.001 ARG H 89 *********************** 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 422 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 377 time to evaluate : 2.498 Fit side-chains REVERT: B 213 ASP cc_start: 0.8787 (p0) cc_final: 0.8577 (p0) REVERT: B 224 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8697 (mtt180) REVERT: B 290 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7478 (ttmt) REVERT: C 200 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7950 (t0) REVERT: D 54 MET cc_start: 0.8311 (mtp) cc_final: 0.8092 (mtp) REVERT: D 180 LYS cc_start: 0.8834 (tptt) cc_final: 0.8461 (tptm) REVERT: D 213 ASP cc_start: 0.8779 (p0) cc_final: 0.8518 (p0) REVERT: E 180 LYS cc_start: 0.8687 (tptt) cc_final: 0.8241 (tptm) REVERT: E 206 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: E 221 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8346 (mtt-85) REVERT: F 213 ASP cc_start: 0.8666 (p0) cc_final: 0.8419 (p0) REVERT: G 59 ASP cc_start: 0.8197 (p0) cc_final: 0.7957 (p0) REVERT: G 180 LYS cc_start: 0.8761 (tptt) cc_final: 0.8211 (tptm) REVERT: H 180 LYS cc_start: 0.8774 (tptt) cc_final: 0.8349 (tptm) REVERT: H 206 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7805 (mt-10) REVERT: I 180 LYS cc_start: 0.8447 (tptt) cc_final: 0.8145 (tptm) REVERT: I 202 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6508 (mt) REVERT: I 246 GLU cc_start: 0.6792 (mp0) cc_final: 0.6430 (mp0) REVERT: I 250 ASP cc_start: 0.7334 (m-30) cc_final: 0.7053 (m-30) outliers start: 45 outliers final: 36 residues processed: 409 average time/residue: 0.4063 time to fit residues: 263.7889 Evaluate side-chains 410 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 369 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 202 LEU 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: 0.9990 chunk 118 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 242 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 ASN F 102 GLN G 127 ASN I 127 ASN J 184 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 30921 Z= 0.175 Angle : 0.909 18.104 43945 Z= 0.351 Chirality : 0.051 0.365 3718 Planarity : 0.005 0.034 5852 Dihedral : 18.900 100.637 4930 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 1.60 % Allowed : 22.28 % Favored : 76.12 % 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: -0.47 (0.17), residues: 2629 helix: 1.57 (0.14), residues: 1342 sheet: None (None), residues: 0 loop : -2.55 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 149 HIS 0.005 0.001 HIS H 171 PHE 0.016 0.001 PHE A 159 TYR 0.012 0.001 TYR E 112 ARG 0.004 0.000 ARG E 116 ********************** 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 381 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 347 time to evaluate : 2.780 Fit side-chains REVERT: A 228 LEU cc_start: 0.8398 (pt) cc_final: 0.8123 (mt) REVERT: B 213 ASP cc_start: 0.8736 (p0) cc_final: 0.8499 (p0) REVERT: B 224 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8551 (mtt180) REVERT: B 290 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7421 (ttmt) REVERT: C 200 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7849 (t0) REVERT: D 54 MET cc_start: 0.8295 (mtp) cc_final: 0.8092 (mtp) REVERT: D 180 LYS cc_start: 0.8805 (tptt) cc_final: 0.8422 (tptm) REVERT: D 213 ASP cc_start: 0.8722 (p0) cc_final: 0.8501 (p0) REVERT: E 180 LYS cc_start: 0.8630 (tptt) cc_final: 0.8326 (tptm) REVERT: E 206 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: F 228 LEU cc_start: 0.8474 (pt) cc_final: 0.8203 (mt) REVERT: G 59 ASP cc_start: 0.8175 (p0) cc_final: 0.7956 (p0) REVERT: G 180 LYS cc_start: 0.8744 (tptt) cc_final: 0.8234 (tptm) REVERT: H 180 LYS cc_start: 0.8787 (tptt) cc_final: 0.8341 (tptm) REVERT: H 206 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7737 (mt-10) REVERT: I 180 LYS cc_start: 0.8437 (tptt) cc_final: 0.8138 (tptm) REVERT: I 246 GLU cc_start: 0.6668 (mp0) cc_final: 0.6280 (mp0) REVERT: I 250 ASP cc_start: 0.7280 (m-30) cc_final: 0.6973 (m-30) REVERT: K 228 LEU cc_start: 0.8466 (pt) cc_final: 0.8257 (mt) outliers start: 34 outliers final: 24 residues processed: 373 average time/residue: 0.4074 time to fit residues: 240.2589 Evaluate side-chains 365 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 338 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 223 CYS Chi-restraints excluded: chain J residue 265 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 127 ASN E 111 ASN F 102 GLN F 184 ASN G 184 ASN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098856 restraints weight = 35407.075| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.72 r_work: 0.2801 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.187 30921 Z= 0.205 Angle : 0.976 59.200 43945 Z= 0.414 Chirality : 0.051 0.365 3718 Planarity : 0.005 0.037 5852 Dihedral : 18.898 100.662 4930 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.41 % Allowed : 22.23 % Favored : 76.35 % 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: 2629 helix: 1.62 (0.14), residues: 1342 sheet: None (None), residues: 0 loop : -2.53 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 149 HIS 0.004 0.001 HIS H 171 PHE 0.015 0.001 PHE A 159 TYR 0.020 0.001 TYR E 112 ARG 0.002 0.000 ARG H 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6115.80 seconds wall clock time: 111 minutes 26.15 seconds (6686.15 seconds total)