Starting phenix.real_space_refine (version: dev) on Sat May 14 04:50:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/05_2022/5wp9_8874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/05_2022/5wp9_8874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/05_2022/5wp9_8874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/05_2022/5wp9_8874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/05_2022/5wp9_8874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/05_2022/5wp9_8874_updated.pdb" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 2.837 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 117048 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "B" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "C" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "D" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "E" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "F" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "G" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "H" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "I" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "J" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "K" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "L" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "M" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "N" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "O" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9471 Classifications: {'peptide': 590} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564, 'PCIS': 1} Chain breaks: 2 Chain: "P" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5127 Classifications: {'peptide': 329} Modifications used: {'NH1NOTPRO': 1, 'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GCP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 38.51, per 1000 atoms: 0.33 Number of scatterers: 117048 At special positions: 0 Unit cell: (153.72, 161.04, 361.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 224 16.00 P 24 15.00 Mg 8 11.99 O 10880 8.00 N 10136 7.00 C 36696 6.00 H 59080 1.00 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=0, symmetry=0 Time building additional restraints: 78.67 Conformation dependent library (CDL) restraints added in 7.0 seconds 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13840 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 256 helices and 32 sheets defined 60.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.98 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 Proline residue: A 6 - end of helix removed outlier: 4.609A pdb=" N PHE A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 47 Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 161 through 175 removed outlier: 4.087A pdb=" N PHE A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.858A pdb=" N GLU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix removed outlier: 4.297A pdb=" N TYR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 removed outlier: 5.254A pdb=" N THR A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 382 removed outlier: 5.078A pdb=" N ILE A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 410 through 450 removed outlier: 4.099A pdb=" N LYS A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 4.013A pdb=" N ILE A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR A 449 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER A 450 " --> pdb=" O CYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG A 456 " --> pdb=" O GLN A 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 459 through 494 Proline residue: A 477 - end of helix removed outlier: 3.749A pdb=" N TYR A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 644 removed outlier: 3.815A pdb=" N ASP A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Proline residue: A 641 - end of helix Processing helix chain 'A' and resid 649 through 660 removed outlier: 3.585A pdb=" N ASP A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 673 removed outlier: 4.050A pdb=" N ASP A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 710 removed outlier: 4.060A pdb=" N GLN A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 19 Proline residue: C 6 - end of helix removed outlier: 4.610A pdb=" N PHE C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C 18 " --> pdb=" O VAL C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 103 through 119 Processing helix chain 'C' and resid 161 through 175 removed outlier: 4.087A pdb=" N PHE C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 3.859A pdb=" N GLU C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 248 through 255 Processing helix chain 'C' and resid 257 through 273 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Proline residue: C 302 - end of helix removed outlier: 4.297A pdb=" N TYR C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 350 removed outlier: 5.254A pdb=" N THR C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 382 removed outlier: 5.077A pdb=" N ILE C 366 " --> pdb=" O GLY C 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 401 Processing helix chain 'C' and resid 410 through 450 removed outlier: 4.098A pdb=" N LYS C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 424 " --> pdb=" O GLN C 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Proline residue: C 427 - end of helix removed outlier: 4.013A pdb=" N ILE C 443 " --> pdb=" O MET C 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR C 449 " --> pdb=" O HIS C 445 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N SER C 450 " --> pdb=" O CYS C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG C 456 " --> pdb=" O GLN C 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 459 through 494 Proline residue: C 477 - end of helix removed outlier: 3.750A pdb=" N TYR C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 644 removed outlier: 3.815A pdb=" N ASP C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Proline residue: C 641 - end of helix Processing helix chain 'C' and resid 649 through 660 removed outlier: 3.585A pdb=" N ASP C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN C 657 " --> pdb=" O LYS C 653 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 673 removed outlier: 4.049A pdb=" N ASP C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 710 removed outlier: 4.060A pdb=" N GLN C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 708 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 Proline residue: E 6 - end of helix removed outlier: 4.610A pdb=" N PHE E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 47 Processing helix chain 'E' and resid 103 through 119 Processing helix chain 'E' and resid 161 through 175 removed outlier: 4.086A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 204 removed outlier: 3.859A pdb=" N GLU E 202 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 301 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Proline residue: E 302 - end of helix removed outlier: 4.298A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 350 removed outlier: 5.254A pdb=" N THR E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 382 removed outlier: 5.077A pdb=" N ILE E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR E 373 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE E 374 " --> pdb=" O PHE E 370 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 401 Processing helix chain 'E' and resid 410 through 450 removed outlier: 4.098A pdb=" N LYS E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 424 " --> pdb=" O GLN E 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU E 426 " --> pdb=" O LYS E 422 " (cutoff:3.500A) Proline residue: E 427 - end of helix removed outlier: 4.013A pdb=" N ILE E 443 " --> pdb=" O MET E 439 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN E 448 " --> pdb=" O GLN E 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR E 449 " --> pdb=" O HIS E 445 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER E 450 " --> pdb=" O CYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG E 456 " --> pdb=" O GLN E 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE E 457 " --> pdb=" O GLU E 453 " (cutoff:3.500A) Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 459 through 494 Proline residue: E 477 - end of helix removed outlier: 3.751A pdb=" N TYR E 493 " --> pdb=" O ILE E 489 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 644 removed outlier: 3.815A pdb=" N ASP E 638 " --> pdb=" O LYS E 634 " (cutoff:3.500A) Proline residue: E 641 - end of helix Processing helix chain 'E' and resid 649 through 660 removed outlier: 3.585A pdb=" N ASP E 654 " --> pdb=" O ASN E 650 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN E 657 " --> pdb=" O LYS E 653 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER E 658 " --> pdb=" O ASP E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 673 removed outlier: 4.050A pdb=" N ASP E 671 " --> pdb=" O SER E 667 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 710 removed outlier: 4.060A pdb=" N GLN E 699 " --> pdb=" O GLN E 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS E 708 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 709 " --> pdb=" O ARG E 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 Proline residue: G 6 - end of helix removed outlier: 4.609A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL G 18 " --> pdb=" O VAL G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 47 Processing helix chain 'G' and resid 103 through 119 Processing helix chain 'G' and resid 161 through 175 removed outlier: 4.086A pdb=" N PHE G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 204 removed outlier: 3.859A pdb=" N GLU G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 248 through 255 Processing helix chain 'G' and resid 257 through 273 Processing helix chain 'G' and resid 276 through 281 Processing helix chain 'G' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 301 " --> pdb=" O ILE G 297 " (cutoff:3.500A) Proline residue: G 302 - end of helix removed outlier: 4.298A pdb=" N TYR G 322 " --> pdb=" O LEU G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 350 removed outlier: 5.253A pdb=" N THR G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 382 removed outlier: 5.077A pdb=" N ILE G 366 " --> pdb=" O GLY G 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR G 373 " --> pdb=" O ILE G 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE G 374 " --> pdb=" O PHE G 370 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G 381 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 401 Processing helix chain 'G' and resid 410 through 450 removed outlier: 4.097A pdb=" N LYS G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G 424 " --> pdb=" O GLN G 420 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 425 " --> pdb=" O ILE G 421 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU G 426 " --> pdb=" O LYS G 422 " (cutoff:3.500A) Proline residue: G 427 - end of helix removed outlier: 4.014A pdb=" N ILE G 443 " --> pdb=" O MET G 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN G 444 " --> pdb=" O GLN G 440 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN G 448 " --> pdb=" O GLN G 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR G 449 " --> pdb=" O HIS G 445 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER G 450 " --> pdb=" O CYS G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG G 456 " --> pdb=" O GLN G 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE G 457 " --> pdb=" O GLU G 453 " (cutoff:3.500A) Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 459 through 494 Proline residue: G 477 - end of helix removed outlier: 3.749A pdb=" N TYR G 493 " --> pdb=" O ILE G 489 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 644 removed outlier: 3.816A pdb=" N ASP G 638 " --> pdb=" O LYS G 634 " (cutoff:3.500A) Proline residue: G 641 - end of helix Processing helix chain 'G' and resid 649 through 660 removed outlier: 3.585A pdb=" N ASP G 654 " --> pdb=" O ASN G 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN G 657 " --> pdb=" O LYS G 653 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER G 658 " --> pdb=" O ASP G 654 " (cutoff:3.500A) Processing helix chain 'G' and resid 666 through 673 removed outlier: 4.050A pdb=" N ASP G 671 " --> pdb=" O SER G 667 " (cutoff:3.500A) Processing helix chain 'G' and resid 677 through 710 removed outlier: 4.059A pdb=" N GLN G 699 " --> pdb=" O GLN G 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS G 708 " --> pdb=" O ILE G 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU G 709 " --> pdb=" O ARG G 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP G 710 " --> pdb=" O GLU G 706 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 19 Proline residue: I 6 - end of helix removed outlier: 4.609A pdb=" N PHE I 15 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL I 18 " --> pdb=" O VAL I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 47 Processing helix chain 'I' and resid 103 through 119 Processing helix chain 'I' and resid 161 through 175 removed outlier: 4.087A pdb=" N PHE I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 204 removed outlier: 3.859A pdb=" N GLU I 202 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 232 Processing helix chain 'I' and resid 248 through 255 Processing helix chain 'I' and resid 257 through 273 Processing helix chain 'I' and resid 276 through 281 Processing helix chain 'I' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS I 300 " --> pdb=" O HIS I 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 301 " --> pdb=" O ILE I 297 " (cutoff:3.500A) Proline residue: I 302 - end of helix removed outlier: 4.298A pdb=" N TYR I 322 " --> pdb=" O LEU I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 350 removed outlier: 5.254A pdb=" N THR I 332 " --> pdb=" O ASP I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 382 removed outlier: 5.077A pdb=" N ILE I 366 " --> pdb=" O GLY I 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR I 373 " --> pdb=" O ILE I 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE I 374 " --> pdb=" O PHE I 370 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL I 381 " --> pdb=" O THR I 377 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP I 382 " --> pdb=" O LEU I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 401 Processing helix chain 'I' and resid 410 through 450 removed outlier: 4.098A pdb=" N LYS I 418 " --> pdb=" O GLU I 414 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU I 424 " --> pdb=" O GLN I 420 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU I 425 " --> pdb=" O ILE I 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU I 426 " --> pdb=" O LYS I 422 " (cutoff:3.500A) Proline residue: I 427 - end of helix removed outlier: 4.014A pdb=" N ILE I 443 " --> pdb=" O MET I 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN I 444 " --> pdb=" O GLN I 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN I 448 " --> pdb=" O GLN I 444 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR I 449 " --> pdb=" O HIS I 445 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER I 450 " --> pdb=" O CYS I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG I 456 " --> pdb=" O GLN I 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE I 457 " --> pdb=" O GLU I 453 " (cutoff:3.500A) Proline residue: I 458 - end of helix Processing helix chain 'I' and resid 459 through 494 Proline residue: I 477 - end of helix removed outlier: 3.750A pdb=" N TYR I 493 " --> pdb=" O ILE I 489 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE I 494 " --> pdb=" O GLU I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 612 through 644 removed outlier: 3.815A pdb=" N ASP I 638 " --> pdb=" O LYS I 634 " (cutoff:3.500A) Proline residue: I 641 - end of helix Processing helix chain 'I' and resid 649 through 660 removed outlier: 3.585A pdb=" N ASP I 654 " --> pdb=" O ASN I 650 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN I 657 " --> pdb=" O LYS I 653 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER I 658 " --> pdb=" O ASP I 654 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 673 removed outlier: 4.050A pdb=" N ASP I 671 " --> pdb=" O SER I 667 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 710 removed outlier: 4.060A pdb=" N GLN I 699 " --> pdb=" O GLN I 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS I 708 " --> pdb=" O ILE I 704 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU I 709 " --> pdb=" O ARG I 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP I 710 " --> pdb=" O GLU I 706 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 19 Proline residue: K 6 - end of helix removed outlier: 4.609A pdb=" N PHE K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL K 18 " --> pdb=" O VAL K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 161 through 175 removed outlier: 4.087A pdb=" N PHE K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 204 removed outlier: 3.858A pdb=" N GLU K 202 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL K 203 " --> pdb=" O ILE K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 232 Processing helix chain 'K' and resid 248 through 255 Processing helix chain 'K' and resid 257 through 273 Processing helix chain 'K' and resid 276 through 281 Processing helix chain 'K' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS K 300 " --> pdb=" O HIS K 296 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 301 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Proline residue: K 302 - end of helix removed outlier: 4.298A pdb=" N TYR K 322 " --> pdb=" O LEU K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 350 removed outlier: 5.254A pdb=" N THR K 332 " --> pdb=" O ASP K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 382 removed outlier: 5.077A pdb=" N ILE K 366 " --> pdb=" O GLY K 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR K 373 " --> pdb=" O ILE K 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE K 374 " --> pdb=" O PHE K 370 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL K 381 " --> pdb=" O THR K 377 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 401 Processing helix chain 'K' and resid 410 through 450 removed outlier: 4.099A pdb=" N LYS K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU K 425 " --> pdb=" O ILE K 421 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU K 426 " --> pdb=" O LYS K 422 " (cutoff:3.500A) Proline residue: K 427 - end of helix removed outlier: 4.014A pdb=" N ILE K 443 " --> pdb=" O MET K 439 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN K 444 " --> pdb=" O GLN K 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN K 448 " --> pdb=" O GLN K 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR K 449 " --> pdb=" O HIS K 445 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER K 450 " --> pdb=" O CYS K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 458 removed outlier: 4.290A pdb=" N ARG K 456 " --> pdb=" O GLN K 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE K 457 " --> pdb=" O GLU K 453 " (cutoff:3.500A) Proline residue: K 458 - end of helix Processing helix chain 'K' and resid 459 through 494 Proline residue: K 477 - end of helix removed outlier: 3.750A pdb=" N TYR K 493 " --> pdb=" O ILE K 489 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE K 494 " --> pdb=" O GLU K 490 " (cutoff:3.500A) Processing helix chain 'K' and resid 612 through 644 removed outlier: 3.815A pdb=" N ASP K 638 " --> pdb=" O LYS K 634 " (cutoff:3.500A) Proline residue: K 641 - end of helix Processing helix chain 'K' and resid 649 through 660 removed outlier: 3.586A pdb=" N ASP K 654 " --> pdb=" O ASN K 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN K 657 " --> pdb=" O LYS K 653 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER K 658 " --> pdb=" O ASP K 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 666 through 673 removed outlier: 4.050A pdb=" N ASP K 671 " --> pdb=" O SER K 667 " (cutoff:3.500A) Processing helix chain 'K' and resid 677 through 710 removed outlier: 4.060A pdb=" N GLN K 699 " --> pdb=" O GLN K 695 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS K 708 " --> pdb=" O ILE K 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU K 709 " --> pdb=" O ARG K 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP K 710 " --> pdb=" O GLU K 706 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 19 Proline residue: M 6 - end of helix removed outlier: 4.610A pdb=" N PHE M 15 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 47 Processing helix chain 'M' and resid 103 through 119 Processing helix chain 'M' and resid 161 through 175 removed outlier: 4.087A pdb=" N PHE M 173 " --> pdb=" O LEU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 removed outlier: 3.859A pdb=" N GLU M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL M 203 " --> pdb=" O ILE M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 232 Processing helix chain 'M' and resid 248 through 255 Processing helix chain 'M' and resid 257 through 273 Processing helix chain 'M' and resid 276 through 281 Processing helix chain 'M' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS M 300 " --> pdb=" O HIS M 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU M 301 " --> pdb=" O ILE M 297 " (cutoff:3.500A) Proline residue: M 302 - end of helix removed outlier: 4.298A pdb=" N TYR M 322 " --> pdb=" O LEU M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 350 removed outlier: 5.254A pdb=" N THR M 332 " --> pdb=" O ASP M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 382 removed outlier: 5.078A pdb=" N ILE M 366 " --> pdb=" O GLY M 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR M 373 " --> pdb=" O ILE M 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE M 374 " --> pdb=" O PHE M 370 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG M 376 " --> pdb=" O GLU M 372 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL M 381 " --> pdb=" O THR M 377 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP M 382 " --> pdb=" O LEU M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 401 Processing helix chain 'M' and resid 410 through 450 removed outlier: 4.097A pdb=" N LYS M 418 " --> pdb=" O GLU M 414 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU M 424 " --> pdb=" O GLN M 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU M 425 " --> pdb=" O ILE M 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU M 426 " --> pdb=" O LYS M 422 " (cutoff:3.500A) Proline residue: M 427 - end of helix removed outlier: 4.013A pdb=" N ILE M 443 " --> pdb=" O MET M 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN M 444 " --> pdb=" O GLN M 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN M 448 " --> pdb=" O GLN M 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR M 449 " --> pdb=" O HIS M 445 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N SER M 450 " --> pdb=" O CYS M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG M 456 " --> pdb=" O GLN M 452 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE M 457 " --> pdb=" O GLU M 453 " (cutoff:3.500A) Proline residue: M 458 - end of helix Processing helix chain 'M' and resid 459 through 494 Proline residue: M 477 - end of helix removed outlier: 3.750A pdb=" N TYR M 493 " --> pdb=" O ILE M 489 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE M 494 " --> pdb=" O GLU M 490 " (cutoff:3.500A) Processing helix chain 'M' and resid 612 through 644 removed outlier: 3.815A pdb=" N ASP M 638 " --> pdb=" O LYS M 634 " (cutoff:3.500A) Proline residue: M 641 - end of helix Processing helix chain 'M' and resid 649 through 660 removed outlier: 3.585A pdb=" N ASP M 654 " --> pdb=" O ASN M 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN M 657 " --> pdb=" O LYS M 653 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER M 658 " --> pdb=" O ASP M 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 673 removed outlier: 4.049A pdb=" N ASP M 671 " --> pdb=" O SER M 667 " (cutoff:3.500A) Processing helix chain 'M' and resid 677 through 710 removed outlier: 4.060A pdb=" N GLN M 699 " --> pdb=" O GLN M 695 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS M 708 " --> pdb=" O ILE M 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU M 709 " --> pdb=" O ARG M 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP M 710 " --> pdb=" O GLU M 706 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 19 Proline residue: O 6 - end of helix removed outlier: 4.609A pdb=" N PHE O 15 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 47 Processing helix chain 'O' and resid 103 through 119 Processing helix chain 'O' and resid 161 through 175 removed outlier: 4.086A pdb=" N PHE O 173 " --> pdb=" O LEU O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 204 removed outlier: 3.859A pdb=" N GLU O 202 " --> pdb=" O LYS O 198 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL O 203 " --> pdb=" O ILE O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 232 Processing helix chain 'O' and resid 248 through 255 Processing helix chain 'O' and resid 257 through 273 Processing helix chain 'O' and resid 276 through 281 Processing helix chain 'O' and resid 282 through 323 removed outlier: 4.185A pdb=" N CYS O 300 " --> pdb=" O HIS O 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU O 301 " --> pdb=" O ILE O 297 " (cutoff:3.500A) Proline residue: O 302 - end of helix removed outlier: 4.297A pdb=" N TYR O 322 " --> pdb=" O LEU O 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 350 removed outlier: 5.253A pdb=" N THR O 332 " --> pdb=" O ASP O 328 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 382 removed outlier: 5.077A pdb=" N ILE O 366 " --> pdb=" O GLY O 362 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR O 373 " --> pdb=" O ILE O 369 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE O 374 " --> pdb=" O PHE O 370 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG O 376 " --> pdb=" O GLU O 372 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL O 381 " --> pdb=" O THR O 377 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP O 382 " --> pdb=" O LEU O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 401 Processing helix chain 'O' and resid 410 through 450 removed outlier: 4.098A pdb=" N LYS O 418 " --> pdb=" O GLU O 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU O 424 " --> pdb=" O GLN O 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU O 425 " --> pdb=" O ILE O 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU O 426 " --> pdb=" O LYS O 422 " (cutoff:3.500A) Proline residue: O 427 - end of helix removed outlier: 4.014A pdb=" N ILE O 443 " --> pdb=" O MET O 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN O 444 " --> pdb=" O GLN O 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN O 448 " --> pdb=" O GLN O 444 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR O 449 " --> pdb=" O HIS O 445 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER O 450 " --> pdb=" O CYS O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 458 removed outlier: 4.291A pdb=" N ARG O 456 " --> pdb=" O GLN O 452 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A) Proline residue: O 458 - end of helix Processing helix chain 'O' and resid 459 through 494 Proline residue: O 477 - end of helix removed outlier: 3.750A pdb=" N TYR O 493 " --> pdb=" O ILE O 489 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE O 494 " --> pdb=" O GLU O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 612 through 644 removed outlier: 3.816A pdb=" N ASP O 638 " --> pdb=" O LYS O 634 " (cutoff:3.500A) Proline residue: O 641 - end of helix Processing helix chain 'O' and resid 649 through 660 removed outlier: 3.586A pdb=" N ASP O 654 " --> pdb=" O ASN O 650 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN O 657 " --> pdb=" O LYS O 653 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER O 658 " --> pdb=" O ASP O 654 " (cutoff:3.500A) Processing helix chain 'O' and resid 666 through 673 removed outlier: 4.049A pdb=" N ASP O 671 " --> pdb=" O SER O 667 " (cutoff:3.500A) Processing helix chain 'O' and resid 677 through 710 removed outlier: 4.059A pdb=" N GLN O 699 " --> pdb=" O GLN O 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS O 708 " --> pdb=" O ILE O 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU O 709 " --> pdb=" O ARG O 705 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP O 710 " --> pdb=" O GLU O 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 142 through 168 Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 216' Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU B 244 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 245' Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 removed outlier: 4.754A pdb=" N SER B 368 " --> pdb=" O CYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 Processing helix chain 'B' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 450 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 180 through 185 removed outlier: 5.622A pdb=" N GLY B 185 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 142 through 168 Processing helix chain 'D' and resid 211 through 216 removed outlier: 3.942A pdb=" N THR D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 211 through 216' Processing helix chain 'D' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU D 244 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 245' Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.882A pdb=" N ASP D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 368 removed outlier: 4.754A pdb=" N SER D 368 " --> pdb=" O CYS D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLU D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 450 Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 180 through 185 removed outlier: 5.622A pdb=" N GLY D 185 " --> pdb=" O GLY D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 180 through 185' Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 142 through 168 Processing helix chain 'F' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL F 216 " --> pdb=" O GLY F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 211 through 216' Processing helix chain 'F' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU F 244 " --> pdb=" O TRP F 240 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 245' Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 267 through 276 Processing helix chain 'F' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP F 349 " --> pdb=" O LEU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 368 removed outlier: 4.753A pdb=" N SER F 368 " --> pdb=" O CYS F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 387 Processing helix chain 'F' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU F 397 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 450 Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 180 through 185 removed outlier: 5.621A pdb=" N GLY F 185 " --> pdb=" O GLY F 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 180 through 185' Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 142 through 168 Processing helix chain 'H' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR H 215 " --> pdb=" O PRO H 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL H 216 " --> pdb=" O GLY H 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 216' Processing helix chain 'H' and resid 240 through 245 removed outlier: 3.856A pdb=" N LEU H 244 " --> pdb=" O TRP H 240 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL H 245 " --> pdb=" O ASP H 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 240 through 245' Processing helix chain 'H' and resid 250 through 264 Processing helix chain 'H' and resid 267 through 276 Processing helix chain 'H' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP H 349 " --> pdb=" O LEU H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 368 removed outlier: 4.753A pdb=" N SER H 368 " --> pdb=" O CYS H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 387 Processing helix chain 'H' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU H 397 " --> pdb=" O THR H 393 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY H 398 " --> pdb=" O GLU H 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU H 399 " --> pdb=" O GLU H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 450 Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 180 through 185 removed outlier: 5.623A pdb=" N GLY H 185 " --> pdb=" O GLY H 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 180 through 185' Processing helix chain 'J' and resid 126 through 138 Processing helix chain 'J' and resid 142 through 168 Processing helix chain 'J' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR J 215 " --> pdb=" O PRO J 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL J 216 " --> pdb=" O GLY J 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 211 through 216' Processing helix chain 'J' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU J 244 " --> pdb=" O TRP J 240 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL J 245 " --> pdb=" O ASP J 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 240 through 245' Processing helix chain 'J' and resid 250 through 264 Processing helix chain 'J' and resid 267 through 276 Processing helix chain 'J' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP J 349 " --> pdb=" O LEU J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 368 removed outlier: 4.754A pdb=" N SER J 368 " --> pdb=" O CYS J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 387 Processing helix chain 'J' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY J 398 " --> pdb=" O GLU J 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU J 399 " --> pdb=" O GLU J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 432 through 450 Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 180 through 185 removed outlier: 5.622A pdb=" N GLY J 185 " --> pdb=" O GLY J 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 180 through 185' Processing helix chain 'L' and resid 126 through 138 Processing helix chain 'L' and resid 142 through 168 Processing helix chain 'L' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR L 215 " --> pdb=" O PRO L 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL L 216 " --> pdb=" O GLY L 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 211 through 216' Processing helix chain 'L' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU L 244 " --> pdb=" O TRP L 240 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL L 245 " --> pdb=" O ASP L 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 240 through 245' Processing helix chain 'L' and resid 250 through 264 Processing helix chain 'L' and resid 267 through 276 Processing helix chain 'L' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 368 removed outlier: 4.754A pdb=" N SER L 368 " --> pdb=" O CYS L 364 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 387 Processing helix chain 'L' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU L 397 " --> pdb=" O THR L 393 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY L 398 " --> pdb=" O GLU L 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU L 399 " --> pdb=" O GLU L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 450 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 180 through 185 removed outlier: 5.622A pdb=" N GLY L 185 " --> pdb=" O GLY L 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 180 through 185' Processing helix chain 'N' and resid 126 through 138 Processing helix chain 'N' and resid 142 through 168 Processing helix chain 'N' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR N 215 " --> pdb=" O PRO N 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL N 216 " --> pdb=" O GLY N 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 216' Processing helix chain 'N' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU N 244 " --> pdb=" O TRP N 240 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL N 245 " --> pdb=" O ASP N 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 240 through 245' Processing helix chain 'N' and resid 250 through 264 Processing helix chain 'N' and resid 267 through 276 Processing helix chain 'N' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP N 349 " --> pdb=" O LEU N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 368 removed outlier: 4.754A pdb=" N SER N 368 " --> pdb=" O CYS N 364 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 387 Processing helix chain 'N' and resid 393 through 415 removed outlier: 3.892A pdb=" N LEU N 397 " --> pdb=" O THR N 393 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY N 398 " --> pdb=" O GLU N 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU N 399 " --> pdb=" O GLU N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 432 through 450 Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 180 through 185 removed outlier: 5.623A pdb=" N GLY N 185 " --> pdb=" O GLY N 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 180 through 185' Processing helix chain 'P' and resid 126 through 138 Processing helix chain 'P' and resid 142 through 168 Processing helix chain 'P' and resid 211 through 216 removed outlier: 3.941A pdb=" N THR P 215 " --> pdb=" O PRO P 211 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL P 216 " --> pdb=" O GLY P 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 211 through 216' Processing helix chain 'P' and resid 240 through 245 removed outlier: 3.857A pdb=" N LEU P 244 " --> pdb=" O TRP P 240 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL P 245 " --> pdb=" O ASP P 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 240 through 245' Processing helix chain 'P' and resid 250 through 264 Processing helix chain 'P' and resid 267 through 276 Processing helix chain 'P' and resid 334 through 350 removed outlier: 3.881A pdb=" N ASP P 349 " --> pdb=" O LEU P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 368 removed outlier: 4.753A pdb=" N SER P 368 " --> pdb=" O CYS P 364 " (cutoff:3.500A) Processing helix chain 'P' and resid 374 through 387 Processing helix chain 'P' and resid 393 through 415 removed outlier: 3.893A pdb=" N LEU P 397 " --> pdb=" O THR P 393 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY P 398 " --> pdb=" O GLU P 394 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU P 399 " --> pdb=" O GLU P 395 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 450 Proline residue: P 450 - end of helix Processing helix chain 'P' and resid 180 through 185 removed outlier: 5.622A pdb=" N GLY P 185 " --> pdb=" O GLY P 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 180 through 185' Processing sheet with id= 1, first strand: chain 'A' and resid 27 through 33 removed outlier: 6.018A pdb=" N ILE A 28 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 146 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 30 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY A 32 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 140 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N HIS A 69 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS A 131 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 180 through 186 Processing sheet with id= 3, first strand: chain 'C' and resid 27 through 33 removed outlier: 6.017A pdb=" N ILE C 28 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP C 146 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 30 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY C 32 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 140 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS C 69 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS C 131 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 180 through 186 Processing sheet with id= 5, first strand: chain 'E' and resid 27 through 33 removed outlier: 6.017A pdb=" N ILE E 28 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP E 146 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL E 30 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY E 32 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL E 140 " --> pdb=" O HIS E 69 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N HIS E 69 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS E 131 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 180 through 186 Processing sheet with id= 7, first strand: chain 'G' and resid 27 through 33 removed outlier: 6.017A pdb=" N ILE G 28 " --> pdb=" O LEU G 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP G 146 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL G 30 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY G 32 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL G 140 " --> pdb=" O HIS G 69 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS G 69 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS G 131 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 180 through 186 Processing sheet with id= 9, first strand: chain 'I' and resid 27 through 33 removed outlier: 6.017A pdb=" N ILE I 28 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP I 146 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 30 " --> pdb=" O ASP I 146 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY I 32 " --> pdb=" O PRO I 148 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL I 140 " --> pdb=" O HIS I 69 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS I 69 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS I 131 " --> pdb=" O LEU I 94 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'I' and resid 180 through 186 Processing sheet with id= 11, first strand: chain 'K' and resid 27 through 33 removed outlier: 6.018A pdb=" N ILE K 28 " --> pdb=" O LEU K 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP K 146 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 30 " --> pdb=" O ASP K 146 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY K 32 " --> pdb=" O PRO K 148 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL K 140 " --> pdb=" O HIS K 69 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS K 69 " --> pdb=" O VAL K 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS K 131 " --> pdb=" O LEU K 94 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'K' and resid 180 through 186 Processing sheet with id= 13, first strand: chain 'M' and resid 27 through 33 removed outlier: 6.017A pdb=" N ILE M 28 " --> pdb=" O LEU M 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP M 146 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL M 30 " --> pdb=" O ASP M 146 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY M 32 " --> pdb=" O PRO M 148 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL M 140 " --> pdb=" O HIS M 69 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS M 69 " --> pdb=" O VAL M 140 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS M 131 " --> pdb=" O LEU M 94 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'M' and resid 180 through 186 Processing sheet with id= 15, first strand: chain 'O' and resid 27 through 33 removed outlier: 6.017A pdb=" N ILE O 28 " --> pdb=" O LEU O 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP O 146 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL O 30 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLY O 32 " --> pdb=" O PRO O 148 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL O 140 " --> pdb=" O HIS O 69 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS O 69 " --> pdb=" O VAL O 140 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS O 131 " --> pdb=" O LEU O 94 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'O' and resid 180 through 186 Processing sheet with id= 17, first strand: chain 'B' and resid 176 through 179 removed outlier: 5.443A pdb=" N GLU B 286 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU B 287 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 278 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 206 through 210 removed outlier: 4.866A pdb=" N LEU B 206 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 176 through 179 removed outlier: 5.443A pdb=" N GLU D 286 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU D 287 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 278 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 206 through 210 removed outlier: 4.865A pdb=" N LEU D 206 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 176 through 179 removed outlier: 5.443A pdb=" N GLU F 286 " --> pdb=" O VAL F 303 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU F 287 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 278 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 206 through 210 removed outlier: 4.866A pdb=" N LEU F 206 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 176 through 179 removed outlier: 5.443A pdb=" N GLU H 286 " --> pdb=" O VAL H 303 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU H 287 " --> pdb=" O SER H 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU H 278 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 206 through 210 removed outlier: 4.866A pdb=" N LEU H 206 " --> pdb=" O THR H 228 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 176 through 179 removed outlier: 5.443A pdb=" N GLU J 286 " --> pdb=" O VAL J 303 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU J 287 " --> pdb=" O SER J 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU J 278 " --> pdb=" O GLU J 291 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 206 through 210 removed outlier: 4.865A pdb=" N LEU J 206 " --> pdb=" O THR J 228 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 176 through 179 removed outlier: 5.442A pdb=" N GLU L 286 " --> pdb=" O VAL L 303 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU L 287 " --> pdb=" O SER L 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU L 278 " --> pdb=" O GLU L 291 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 206 through 210 removed outlier: 4.866A pdb=" N LEU L 206 " --> pdb=" O THR L 228 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 176 through 179 removed outlier: 5.442A pdb=" N GLU N 286 " --> pdb=" O VAL N 303 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU N 287 " --> pdb=" O SER N 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU N 278 " --> pdb=" O GLU N 291 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 206 through 210 removed outlier: 4.866A pdb=" N LEU N 206 " --> pdb=" O THR N 228 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 176 through 179 removed outlier: 5.443A pdb=" N GLU P 286 " --> pdb=" O VAL P 303 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU P 287 " --> pdb=" O SER P 282 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU P 278 " --> pdb=" O GLU P 291 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 206 through 210 removed outlier: 4.865A pdb=" N LEU P 206 " --> pdb=" O THR P 228 " (cutoff:3.500A) 3264 hydrogen bonds defined for protein. 9768 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: 44.91 Time building geometry restraints manager: 83.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 58960 1.13 - 1.30: 9864 1.30 - 1.47: 22066 1.47 - 1.64: 26790 1.64 - 1.82: 344 Bond restraints: 118024 Sorted by residual: bond pdb=" CE1 HIS H 348 " pdb=" HE1 HIS H 348 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" CE1 HIS D 348 " pdb=" HE1 HIS D 348 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" CE1 HIS J 348 " pdb=" HE1 HIS J 348 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CE1 HIS P 348 " pdb=" HE1 HIS P 348 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CE1 HIS N 348 " pdb=" HE1 HIS N 348 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 ... (remaining 118019 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.90: 933 103.90 - 112.09: 139263 112.09 - 120.29: 46531 120.29 - 128.49: 27185 128.49 - 136.68: 480 Bond angle restraints: 214392 Sorted by residual: angle pdb=" C GLY F 180 " pdb=" N PRO F 181 " pdb=" CA PRO F 181 " ideal model delta sigma weight residual 119.84 128.70 -8.86 1.25e+00 6.40e-01 5.03e+01 angle pdb=" C GLY B 180 " pdb=" N PRO B 181 " pdb=" CA PRO B 181 " ideal model delta sigma weight residual 119.84 128.69 -8.85 1.25e+00 6.40e-01 5.01e+01 angle pdb=" C GLY E 401 " pdb=" N PRO E 402 " pdb=" CA PRO E 402 " ideal model delta sigma weight residual 119.56 126.78 -7.22 1.02e+00 9.61e-01 5.01e+01 angle pdb=" C GLY L 180 " pdb=" N PRO L 181 " pdb=" CA PRO L 181 " ideal model delta sigma weight residual 119.84 128.67 -8.83 1.25e+00 6.40e-01 4.99e+01 angle pdb=" C GLY G 401 " pdb=" N PRO G 402 " pdb=" CA PRO G 402 " ideal model delta sigma weight residual 119.56 126.76 -7.20 1.02e+00 9.61e-01 4.98e+01 ... (remaining 214387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 45289 16.60 - 33.20: 1043 33.20 - 49.80: 232 49.80 - 66.40: 124 66.40 - 83.00: 16 Dihedral angle restraints: 46704 sinusoidal: 22896 harmonic: 23808 Sorted by residual: dihedral pdb=" CA VAL K 411 " pdb=" C VAL K 411 " pdb=" N SER K 412 " pdb=" CA SER K 412 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA VAL I 411 " pdb=" C VAL I 411 " pdb=" N SER I 412 " pdb=" CA SER I 412 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA VAL O 411 " pdb=" C VAL O 411 " pdb=" N SER O 412 " pdb=" CA SER O 412 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 46701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 5719 0.041 - 0.082: 2421 0.082 - 0.123: 1186 0.123 - 0.165: 91 0.165 - 0.206: 23 Chirality restraints: 9440 Sorted by residual: chirality pdb=" CA VAL J 307 " pdb=" N VAL J 307 " pdb=" C VAL J 307 " pdb=" CB VAL J 307 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL L 307 " pdb=" N VAL L 307 " pdb=" C VAL L 307 " pdb=" CB VAL L 307 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL H 307 " pdb=" N VAL H 307 " pdb=" C VAL H 307 " pdb=" CB VAL H 307 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 9437 not shown) Planarity restraints: 17272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 69 " 0.058 2.00e-02 2.50e+03 6.01e-02 8.12e+01 pdb=" CG HIS I 69 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS I 69 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 HIS I 69 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS I 69 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS I 69 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 HIS I 69 " -0.139 2.00e-02 2.50e+03 pdb=" HD2 HIS I 69 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 HIS I 69 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 69 " 0.057 2.00e-02 2.50e+03 6.01e-02 8.11e+01 pdb=" CG HIS E 69 " 0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS E 69 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 HIS E 69 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS E 69 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS E 69 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 HIS E 69 " -0.139 2.00e-02 2.50e+03 pdb=" HD2 HIS E 69 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 HIS E 69 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 69 " 0.057 2.00e-02 2.50e+03 6.00e-02 8.10e+01 pdb=" CG HIS G 69 " 0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS G 69 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 HIS G 69 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS G 69 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS G 69 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 HIS G 69 " -0.139 2.00e-02 2.50e+03 pdb=" HD2 HIS G 69 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 HIS G 69 " 0.045 2.00e-02 2.50e+03 ... (remaining 17269 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 2581 1.94 - 2.61: 138440 2.61 - 3.27: 386016 3.27 - 3.94: 482914 3.94 - 4.60: 744033 Nonbonded interactions: 1753984 Sorted by model distance: nonbonded pdb=" OE1 GLN M 657 " pdb=" H GLN M 657 " model vdw 1.278 1.850 nonbonded pdb=" OE1 GLN K 657 " pdb=" H GLN K 657 " model vdw 1.279 1.850 nonbonded pdb=" OE1 GLN O 657 " pdb=" H GLN O 657 " model vdw 1.279 1.850 nonbonded pdb=" OE1 GLN A 657 " pdb=" H GLN A 657 " model vdw 1.279 1.850 nonbonded pdb=" OE1 GLN G 657 " pdb=" H GLN G 657 " model vdw 1.279 1.850 ... (remaining 1753979 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 224 5.16 5 C 36696 2.51 5 N 10136 2.21 5 O 10880 1.98 5 H 59080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 1.320 Extract box with map and model: 16.720 Check model and map are aligned: 1.250 Convert atoms to be neutral: 0.750 Process input model: 287.420 Find NCS groups from input model: 4.400 Set up NCS constraints: 0.720 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 317.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 0.011 0.089 58944 Z= 0.749 Angle : 1.242 11.774 80072 Z= 0.778 Chirality : 0.052 0.206 9440 Planarity : 0.022 0.145 10304 Dihedral : 10.028 83.002 22192 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 1.43 % Allowed : 5.46 % Favored : 93.11 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.58 (0.09), residues: 7288 helix: 0.15 (0.07), residues: 4008 sheet: -1.55 (0.23), residues: 488 loop : -0.78 (0.12), residues: 2792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3470 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 3430 time to evaluate : 6.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 12 residues processed: 3466 average time/residue: 1.5607 time to fit residues: 8616.1260 Evaluate side-chains 2659 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 2647 time to evaluate : 6.922 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.9509 time to fit residues: 31.5440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 5.9990 chunk 551 optimal weight: 5.9990 chunk 306 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 372 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 570 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 661 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 HIS B 161 GLN C 9 ASN C 95 HIS C 270 GLN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN D 267 ASN D 294 HIS D 348 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN F 267 ASN F 414 GLN G 9 ASN G 314 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 GLN ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 GLN L 294 HIS L 377 HIS ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 GLN N 294 HIS ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 ASN ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 GLN P 229 GLN P 294 HIS P 348 HIS P 380 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 58944 Z= 0.309 Angle : 0.649 8.168 80072 Z= 0.374 Chirality : 0.040 0.174 9440 Planarity : 0.011 0.094 10304 Dihedral : 5.434 65.324 8024 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.87 % Favored : 95.75 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.30 (0.09), residues: 7288 helix: 0.37 (0.08), residues: 4064 sheet: -1.33 (0.20), residues: 600 loop : -0.62 (0.12), residues: 2624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2997 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2995 time to evaluate : 6.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2996 average time/residue: 1.4775 time to fit residues: 7307.9028 Evaluate side-chains 2569 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2568 time to evaluate : 6.896 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0426 time to fit residues: 10.9621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 550 optimal weight: 5.9990 chunk 450 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 662 optimal weight: 5.9990 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 1.9990 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 531 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 27 GLN A 270 GLN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS C 27 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 270 GLN E 295 HIS ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 HIS G 27 GLN G 270 GLN G 708 HIS I 9 ASN I 27 GLN I 95 HIS ** I 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 GLN K 27 GLN K 95 HIS K 270 GLN ** K 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 708 HIS M 27 GLN M 270 GLN ** M 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 GLN O 27 GLN O 95 HIS ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 480 ASN ** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 58944 Z= 0.384 Angle : 0.736 7.755 80072 Z= 0.416 Chirality : 0.040 0.318 9440 Planarity : 0.008 0.093 10304 Dihedral : 5.361 43.574 8024 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.63 % Favored : 93.99 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.09), residues: 7288 helix: -0.28 (0.07), residues: 4128 sheet: -1.49 (0.19), residues: 600 loop : -0.81 (0.12), residues: 2560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2827 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2823 time to evaluate : 6.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 2825 average time/residue: 1.4703 time to fit residues: 6832.1697 Evaluate side-chains 2495 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2492 time to evaluate : 6.812 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.1006 time to fit residues: 15.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 10.0000 chunk 497 optimal weight: 2.9990 chunk 343 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 0.7980 chunk 664 optimal weight: 0.0980 chunk 703 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN C 95 HIS C 708 HIS D 187 GLN E 27 GLN E 254 ASN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN G 27 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 HIS I 249 GLN I 254 ASN ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 ASN M 249 GLN ** M 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 229 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 58944 Z= 0.196 Angle : 0.555 7.477 80072 Z= 0.301 Chirality : 0.039 0.152 9440 Planarity : 0.006 0.077 10304 Dihedral : 4.907 35.310 8024 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.05 % Favored : 95.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.18 (0.10), residues: 7288 helix: 0.52 (0.08), residues: 4072 sheet: -1.44 (0.20), residues: 600 loop : -0.62 (0.13), residues: 2616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2811 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2811 time to evaluate : 6.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2811 average time/residue: 1.4623 time to fit residues: 6810.2872 Evaluate side-chains 2530 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2530 time to evaluate : 6.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 523 optimal weight: 7.9990 chunk 290 optimal weight: 9.9990 chunk 600 optimal weight: 0.9980 chunk 486 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 chunk 631 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN C 249 GLN C 635 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN E 420 GLN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 HIS ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 708 HIS O 66 GLN ** O 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 58944 Z= 0.203 Angle : 0.554 7.528 80072 Z= 0.299 Chirality : 0.039 0.170 9440 Planarity : 0.006 0.072 10304 Dihedral : 4.645 31.865 8024 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.08 (0.10), residues: 7288 helix: 0.82 (0.08), residues: 4048 sheet: -1.45 (0.20), residues: 576 loop : -0.65 (0.13), residues: 2664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2759 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2759 time to evaluate : 6.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2759 average time/residue: 1.4284 time to fit residues: 6469.1766 Evaluate side-chains 2500 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2500 time to evaluate : 6.893 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.0134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 0.3980 chunk 633 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 413 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 8.9990 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 369 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN E 420 GLN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 635 ASN I 420 GLN K 9 ASN M 9 ASN M 290 ASN ** M 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 ASN O 290 ASN O 420 GLN ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 58944 Z= 0.189 Angle : 0.544 7.861 80072 Z= 0.292 Chirality : 0.039 0.184 9440 Planarity : 0.005 0.071 10304 Dihedral : 4.493 30.121 8024 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.32 (0.10), residues: 7288 helix: 1.03 (0.08), residues: 4056 sheet: -1.45 (0.20), residues: 576 loop : -0.55 (0.13), residues: 2656 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2768 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2768 time to evaluate : 6.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2768 average time/residue: 1.4102 time to fit residues: 6419.3781 Evaluate side-chains 2494 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2494 time to evaluate : 6.830 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 0.5980 chunk 514 optimal weight: 8.9990 chunk 398 optimal weight: 1.9990 chunk 592 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 701 optimal weight: 2.9990 chunk 439 optimal weight: 1.9990 chunk 427 optimal weight: 0.8980 chunk 323 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN G 249 GLN ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 GLN K 448 ASN ** L 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 316 GLN O 320 ASN ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 58944 Z= 0.198 Angle : 0.544 7.777 80072 Z= 0.293 Chirality : 0.039 0.148 9440 Planarity : 0.005 0.071 10304 Dihedral : 4.421 30.204 8024 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.32 % Favored : 95.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.43 (0.10), residues: 7288 helix: 1.11 (0.08), residues: 4064 sheet: -1.36 (0.20), residues: 576 loop : -0.50 (0.13), residues: 2648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2769 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2769 time to evaluate : 6.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2769 average time/residue: 1.4173 time to fit residues: 6468.4484 Evaluate side-chains 2517 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2517 time to evaluate : 6.830 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 419 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 0.0030 chunk 65 optimal weight: 20.0000 chunk 551 optimal weight: 0.8980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 290 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 290 ASN I 335 GLN I 420 GLN K 27 GLN K 249 GLN K 448 ASN L 229 GLN M 420 GLN ** N 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 440 GLN O 448 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 58944 Z= 0.163 Angle : 0.523 8.129 80072 Z= 0.276 Chirality : 0.039 0.168 9440 Planarity : 0.005 0.073 10304 Dihedral : 4.290 29.359 8024 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.69 % Favored : 96.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.81 (0.10), residues: 7288 helix: 1.45 (0.08), residues: 4024 sheet: -1.26 (0.21), residues: 576 loop : -0.36 (0.13), residues: 2688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2785 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2785 time to evaluate : 6.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2785 average time/residue: 1.4440 time to fit residues: 6641.9724 Evaluate side-chains 2501 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2501 time to evaluate : 6.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 3.9990 chunk 672 optimal weight: 2.9990 chunk 613 optimal weight: 0.9980 chunk 653 optimal weight: 4.9990 chunk 393 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 513 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 590 optimal weight: 2.9990 chunk 618 optimal weight: 4.9990 chunk 651 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 420 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN E 398 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN K 448 ASN L 161 GLN O 314 GLN O 420 GLN ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 448 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 58944 Z= 0.188 Angle : 0.537 7.361 80072 Z= 0.287 Chirality : 0.038 0.153 9440 Planarity : 0.005 0.082 10304 Dihedral : 4.279 29.967 8024 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.10 % Favored : 95.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.74 (0.10), residues: 7288 helix: 1.41 (0.08), residues: 4048 sheet: -1.19 (0.21), residues: 576 loop : -0.46 (0.13), residues: 2664 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2761 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2761 time to evaluate : 6.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2761 average time/residue: 1.3995 time to fit residues: 6360.8922 Evaluate side-chains 2508 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2508 time to evaluate : 6.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 20.0000 chunk 691 optimal weight: 0.6980 chunk 422 optimal weight: 1.9990 chunk 328 optimal weight: 0.0370 chunk 480 optimal weight: 5.9990 chunk 725 optimal weight: 9.9990 chunk 667 optimal weight: 3.9990 chunk 577 optimal weight: 0.0870 chunk 59 optimal weight: 9.9990 chunk 446 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN K 448 ASN ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.8075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 58944 Z= 0.178 Angle : 0.531 9.008 80072 Z= 0.283 Chirality : 0.038 0.155 9440 Planarity : 0.005 0.077 10304 Dihedral : 4.258 30.185 8024 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.81 % Favored : 95.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.82 (0.10), residues: 7288 helix: 1.49 (0.08), residues: 4048 sheet: -1.15 (0.21), residues: 576 loop : -0.45 (0.13), residues: 2664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14576 Ramachandran restraints generated. 7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2779 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2779 time to evaluate : 6.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2779 average time/residue: 1.3627 time to fit residues: 6226.9655 Evaluate side-chains 2519 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2519 time to evaluate : 6.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 9.9990 chunk 615 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 532 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 578 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 448 ASN M 295 HIS ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.140052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.089846 restraints weight = 394185.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.096073 restraints weight = 190725.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.100213 restraints weight = 113801.114| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 58944 Z= 0.188 Angle : 0.534 7.342 80072 Z= 0.286 Chirality : 0.039 0.185 9440 Planarity : 0.005 0.087 10304 Dihedral : 4.246 30.168 8024 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.80 (0.10), residues: 7288 helix: 1.49 (0.08), residues: 4048 sheet: -1.02 (0.21), residues: 600 loop : -0.51 (0.13), residues: 2640 =============================================================================== Job complete usr+sys time: 76469.77 seconds wall clock time: 1284 minutes 51.06 seconds (77091.06 seconds total)