Starting phenix.real_space_refine on Thu Feb 15 04:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/02_2024/5wp9_8874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/02_2024/5wp9_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_8874/02_2024/5wp9_8874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/02_2024/5wp9_8874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/02_2024/5wp9_8874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/02_2024/5wp9_8874_updated.pdb" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564} 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: {'COO': 1, 'NH1NOTPRO': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 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: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 35.14, per 1000 atoms: 0.30 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: 71.54 Conformation dependent library (CDL) restraints added in 8.8 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 for structures that cannot fit in PDB format. 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: 23.64 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: 41.76 Time building geometry restraints manager: 75.87 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: 52025 16.60 - 33.20: 1667 33.20 - 49.80: 620 49.80 - 66.40: 540 66.40 - 83.00: 44 Dihedral angle restraints: 54896 sinusoidal: 31088 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 54893 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 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: 1.740 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: 1.240 Extract box with map and model: 11.780 Check model and map are aligned: 1.220 Set scattering table: 0.760 Process input model: 288.230 Find NCS groups from input model: 4.330 Set up NCS constraints: 0.730 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 312.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 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 : 11.154 83.002 22416 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 1.43 % Allowed : 5.46 % Favored : 93.11 % Rotamer: Outliers : 0.63 % Allowed : 0.25 % Favored : 99.12 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.006 TRP J 268 HIS 0.005 0.001 HIS M 651 PHE 0.013 0.003 PHE A 268 TYR 0.025 0.004 TYR C 628 ARG 0.003 0.000 ARG I 633 *********************** 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 : 6.400 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: 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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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8939 (p0) cc_final: 0.8726 (p0) REVERT: A 214 ILE cc_start: 0.9490 (mt) cc_final: 0.9286 (mt) REVERT: A 218 ASP cc_start: 0.8509 (p0) cc_final: 0.8263 (p0) REVERT: A 250 LEU cc_start: 0.9616 (mt) cc_final: 0.9320 (mt) REVERT: A 254 ASN cc_start: 0.8739 (m-40) cc_final: 0.8490 (t0) REVERT: A 288 THR cc_start: 0.9546 (m) cc_final: 0.9334 (m) REVERT: A 295 HIS cc_start: 0.8918 (m-70) cc_final: 0.8623 (m170) REVERT: A 302 PRO cc_start: 0.9294 (OUTLIER) cc_final: 0.8887 (Cg_endo) REVERT: A 442 ILE cc_start: 0.9249 (mt) cc_final: 0.8972 (mt) REVERT: A 448 ASN cc_start: 0.8984 (m-40) cc_final: 0.8752 (m110) REVERT: A 468 VAL cc_start: 0.9231 (t) cc_final: 0.9017 (t) REVERT: A 618 CYS cc_start: 0.8822 (t) cc_final: 0.8493 (p) REVERT: A 619 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8481 (tm-30) REVERT: B 129 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7230 (tm-30) REVERT: B 152 LEU cc_start: 0.8850 (mt) cc_final: 0.8615 (mt) REVERT: B 155 ASP cc_start: 0.9164 (m-30) cc_final: 0.8608 (m-30) REVERT: B 168 PHE cc_start: 0.8636 (m-80) cc_final: 0.8276 (m-80) REVERT: B 209 LEU cc_start: 0.7987 (tp) cc_final: 0.7520 (tp) REVERT: B 219 ASP cc_start: 0.8259 (t0) cc_final: 0.7960 (t0) REVERT: B 289 LEU cc_start: 0.7697 (tp) cc_final: 0.7478 (tp) REVERT: B 417 LEU cc_start: 0.8668 (tp) cc_final: 0.8283 (tp) REVERT: C 18 VAL cc_start: 0.9519 (m) cc_final: 0.9310 (m) REVERT: C 139 VAL cc_start: 0.9213 (m) cc_final: 0.9004 (p) REVERT: C 178 ASN cc_start: 0.7972 (t0) cc_final: 0.7566 (t0) REVERT: C 250 LEU cc_start: 0.9561 (mt) cc_final: 0.9241 (mt) REVERT: C 288 THR cc_start: 0.9546 (m) cc_final: 0.9313 (m) REVERT: C 439 MET cc_start: 0.8702 (mmm) cc_final: 0.8480 (mmm) REVERT: C 448 ASN cc_start: 0.9094 (m-40) cc_final: 0.8807 (m110) REVERT: C 618 CYS cc_start: 0.9037 (t) cc_final: 0.8200 (t) REVERT: C 619 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8767 (tm-30) REVERT: D 134 PHE cc_start: 0.5728 (t80) cc_final: 0.5499 (t80) REVERT: D 148 LEU cc_start: 0.8675 (mt) cc_final: 0.8199 (tt) REVERT: D 155 ASP cc_start: 0.9235 (m-30) cc_final: 0.8701 (m-30) REVERT: D 165 ARG cc_start: 0.8914 (mtt180) cc_final: 0.8503 (tpp80) REVERT: D 168 PHE cc_start: 0.8616 (m-80) cc_final: 0.8367 (m-80) REVERT: D 219 ASP cc_start: 0.8295 (t0) cc_final: 0.7958 (t0) REVERT: D 252 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8195 (ttp80) REVERT: D 417 LEU cc_start: 0.8724 (tp) cc_final: 0.8232 (tp) REVERT: E 178 ASN cc_start: 0.8343 (t0) cc_final: 0.8054 (t0) REVERT: E 295 HIS cc_start: 0.8910 (m-70) cc_final: 0.8494 (m170) REVERT: E 342 THR cc_start: 0.9338 (m) cc_final: 0.9100 (m) REVERT: E 398 ASN cc_start: 0.8717 (m-40) cc_final: 0.8415 (m110) REVERT: E 438 GLU cc_start: 0.8342 (tp30) cc_final: 0.8057 (tp30) REVERT: E 618 CYS cc_start: 0.8767 (t) cc_final: 0.7675 (t) REVERT: E 619 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8591 (tm-30) REVERT: E 660 LEU cc_start: 0.8834 (mt) cc_final: 0.8435 (mt) REVERT: F 129 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7154 (tp30) REVERT: F 134 PHE cc_start: 0.6752 (t80) cc_final: 0.6429 (t80) REVERT: F 155 ASP cc_start: 0.9237 (m-30) cc_final: 0.8998 (m-30) REVERT: F 268 TRP cc_start: 0.8027 (m100) cc_final: 0.7797 (m100) REVERT: G 139 VAL cc_start: 0.9370 (m) cc_final: 0.9166 (p) REVERT: G 250 LEU cc_start: 0.9550 (mt) cc_final: 0.9162 (mp) REVERT: G 448 ASN cc_start: 0.8939 (m-40) cc_final: 0.8729 (m110) REVERT: G 467 VAL cc_start: 0.9203 (t) cc_final: 0.8975 (t) REVERT: G 501 PHE cc_start: 0.7708 (t80) cc_final: 0.7358 (t80) REVERT: G 618 CYS cc_start: 0.8908 (t) cc_final: 0.8096 (p) REVERT: G 619 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8526 (tm-30) REVERT: G 660 LEU cc_start: 0.8790 (mt) cc_final: 0.8554 (mt) REVERT: H 129 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7443 (tp30) REVERT: H 134 PHE cc_start: 0.5863 (t80) cc_final: 0.5639 (t80) REVERT: H 155 ASP cc_start: 0.9423 (m-30) cc_final: 0.8736 (m-30) REVERT: H 219 ASP cc_start: 0.8464 (t0) cc_final: 0.8105 (t0) REVERT: H 267 ASN cc_start: 0.8414 (t0) cc_final: 0.8142 (t0) REVERT: H 280 ARG cc_start: 0.6747 (ppt170) cc_final: 0.6509 (ppt170) REVERT: H 289 LEU cc_start: 0.7702 (tp) cc_final: 0.7354 (tp) REVERT: I 142 LEU cc_start: 0.8889 (tp) cc_final: 0.8629 (tp) REVERT: I 178 ASN cc_start: 0.8216 (t0) cc_final: 0.7950 (t0) REVERT: I 266 TYR cc_start: 0.8057 (t80) cc_final: 0.7646 (t80) REVERT: I 346 ASN cc_start: 0.8951 (m-40) cc_final: 0.8741 (m110) REVERT: I 448 ASN cc_start: 0.9158 (m-40) cc_final: 0.8836 (m110) REVERT: I 501 PHE cc_start: 0.7746 (t80) cc_final: 0.7482 (t80) REVERT: I 618 CYS cc_start: 0.8712 (t) cc_final: 0.7741 (t) REVERT: I 619 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8693 (tm-30) REVERT: I 660 LEU cc_start: 0.8699 (mt) cc_final: 0.8485 (mt) REVERT: J 129 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7588 (tm-30) REVERT: J 155 ASP cc_start: 0.9201 (m-30) cc_final: 0.8966 (m-30) REVERT: J 159 GLU cc_start: 0.9431 (mm-30) cc_final: 0.8718 (mm-30) REVERT: J 163 TYR cc_start: 0.8510 (m-80) cc_final: 0.7719 (m-10) REVERT: J 168 PHE cc_start: 0.8629 (m-80) cc_final: 0.8391 (m-80) REVERT: J 233 CYS cc_start: 0.7559 (t) cc_final: 0.6765 (p) REVERT: J 269 PRO cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (Cg_endo) REVERT: J 402 LEU cc_start: 0.8335 (mt) cc_final: 0.8128 (tp) REVERT: J 417 LEU cc_start: 0.8875 (tp) cc_final: 0.8599 (tp) REVERT: K 139 VAL cc_start: 0.9482 (m) cc_final: 0.9256 (p) REVERT: K 178 ASN cc_start: 0.8352 (t0) cc_final: 0.7915 (t0) REVERT: K 250 LEU cc_start: 0.9508 (mt) cc_final: 0.9056 (mp) REVERT: K 288 THR cc_start: 0.9574 (m) cc_final: 0.9364 (m) REVERT: K 438 GLU cc_start: 0.8290 (tp30) cc_final: 0.8002 (tp30) REVERT: K 439 MET cc_start: 0.8571 (mmm) cc_final: 0.8085 (mmm) REVERT: K 448 ASN cc_start: 0.8929 (m-40) cc_final: 0.8559 (m110) REVERT: K 617 ASP cc_start: 0.8734 (m-30) cc_final: 0.8443 (m-30) REVERT: K 618 CYS cc_start: 0.8973 (t) cc_final: 0.8180 (p) REVERT: K 619 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8675 (tm-30) REVERT: K 660 LEU cc_start: 0.8715 (mt) cc_final: 0.8373 (mt) REVERT: L 129 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7055 (tp30) REVERT: L 134 PHE cc_start: 0.6687 (t80) cc_final: 0.6201 (t80) REVERT: L 148 LEU cc_start: 0.8595 (mt) cc_final: 0.8164 (tt) REVERT: L 152 LEU cc_start: 0.8684 (mt) cc_final: 0.8321 (mt) REVERT: L 155 ASP cc_start: 0.9294 (m-30) cc_final: 0.8457 (m-30) REVERT: L 159 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8275 (mm-30) REVERT: L 163 TYR cc_start: 0.8212 (m-80) cc_final: 0.7347 (m-10) REVERT: L 209 LEU cc_start: 0.7978 (tp) cc_final: 0.7747 (tp) REVERT: L 275 LEU cc_start: 0.7141 (mt) cc_final: 0.5967 (tt) REVERT: L 280 ARG cc_start: 0.7091 (ppt170) cc_final: 0.6847 (ppt170) REVERT: L 289 LEU cc_start: 0.7635 (tp) cc_final: 0.7310 (tp) REVERT: L 417 LEU cc_start: 0.8776 (tp) cc_final: 0.8399 (tp) REVERT: L 427 LEU cc_start: 0.7009 (mp) cc_final: 0.6794 (mp) REVERT: M 139 VAL cc_start: 0.9355 (m) cc_final: 0.9122 (p) REVERT: M 178 ASN cc_start: 0.8148 (t0) cc_final: 0.7819 (t0) REVERT: M 218 ASP cc_start: 0.8349 (p0) cc_final: 0.8006 (p0) REVERT: M 250 LEU cc_start: 0.9579 (mt) cc_final: 0.9341 (mt) REVERT: M 448 ASN cc_start: 0.9189 (m-40) cc_final: 0.8874 (m110) REVERT: M 618 CYS cc_start: 0.8980 (t) cc_final: 0.8404 (p) REVERT: M 619 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8683 (tm-30) REVERT: M 642 LYS cc_start: 0.9003 (mttt) cc_final: 0.8309 (tttt) REVERT: N 129 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7364 (tp30) REVERT: N 134 PHE cc_start: 0.5397 (t80) cc_final: 0.5190 (t80) REVERT: N 148 LEU cc_start: 0.8541 (mt) cc_final: 0.7964 (tt) REVERT: N 155 ASP cc_start: 0.9203 (m-30) cc_final: 0.8702 (m-30) REVERT: N 159 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8526 (mm-30) REVERT: N 163 TYR cc_start: 0.8530 (m-80) cc_final: 0.7647 (m-10) REVERT: N 168 PHE cc_start: 0.8686 (m-80) cc_final: 0.8350 (m-80) REVERT: N 219 ASP cc_start: 0.8414 (t0) cc_final: 0.8114 (t0) REVERT: N 233 CYS cc_start: 0.7737 (t) cc_final: 0.7172 (t) REVERT: N 345 LEU cc_start: 0.5694 (mt) cc_final: 0.5487 (mt) REVERT: O 131 HIS cc_start: 0.7723 (t70) cc_final: 0.7443 (t-170) REVERT: O 178 ASN cc_start: 0.8431 (t0) cc_final: 0.8100 (t0) REVERT: O 254 ASN cc_start: 0.8774 (m-40) cc_final: 0.8468 (t0) REVERT: O 301 LEU cc_start: 0.9099 (mt) cc_final: 0.8761 (mp) REVERT: O 342 THR cc_start: 0.9398 (m) cc_final: 0.9126 (m) REVERT: O 618 CYS cc_start: 0.8926 (t) cc_final: 0.8190 (p) REVERT: O 619 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8591 (tm-30) REVERT: O 642 LYS cc_start: 0.9074 (mttt) cc_final: 0.8385 (tttt) REVERT: P 129 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6952 (tp30) REVERT: P 134 PHE cc_start: 0.6280 (t80) cc_final: 0.6004 (t80) REVERT: P 148 LEU cc_start: 0.8536 (mt) cc_final: 0.8127 (mp) REVERT: P 155 ASP cc_start: 0.9281 (m-30) cc_final: 0.8868 (m-30) REVERT: P 176 PHE cc_start: 0.7429 (m-10) cc_final: 0.6964 (m-10) REVERT: P 229 GLN cc_start: 0.9216 (mt0) cc_final: 0.8860 (tt0) REVERT: P 289 LEU cc_start: 0.7532 (tp) cc_final: 0.7306 (tp) REVERT: P 345 LEU cc_start: 0.5026 (mt) cc_final: 0.4592 (mt) outliers start: 40 outliers final: 13 residues processed: 3466 average time/residue: 1.5158 time to fit residues: 8245.3630 Evaluate side-chains 2677 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2662 time to evaluate : 6.445 ------------------------------------------------------------------------------- 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: 6.9990 chunk 551 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 570 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 346 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 95 HIS A 270 GLN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 294 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 95 HIS ** 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 270 GLN G 314 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN I 9 ASN I 270 GLN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 GLN ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 GLN L 294 HIS L 377 HIS M 9 ASN ** M 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 GLN N 294 HIS N 380 GLN O 9 ASN ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS P 348 HIS P 380 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 58944 Z= 0.351 Angle : 0.683 9.200 80072 Z= 0.393 Chirality : 0.040 0.176 9440 Planarity : 0.010 0.075 10304 Dihedral : 6.727 62.749 8248 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.06 % Favored : 95.55 % Rotamer: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.08 % 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: -0.53 (0.09), residues: 7288 helix: 0.12 (0.07), residues: 4144 sheet: -1.38 (0.20), residues: 600 loop : -0.65 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 268 HIS 0.010 0.002 HIS D 348 PHE 0.016 0.002 PHE O 647 TYR 0.023 0.002 TYR O 449 ARG 0.011 0.001 ARG E 403 *********************** 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 3008 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3006 time to evaluate : 6.419 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 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8990 (mt) cc_final: 0.8632 (mp) REVERT: A 93 PHE cc_start: 0.8157 (m-80) cc_final: 0.6882 (m-80) REVERT: A 110 GLU cc_start: 0.8184 (tt0) cc_final: 0.7661 (tt0) REVERT: A 250 LEU cc_start: 0.9655 (mt) cc_final: 0.9337 (mt) REVERT: A 254 ASN cc_start: 0.8885 (m-40) cc_final: 0.8463 (t0) REVERT: A 336 LEU cc_start: 0.9180 (mt) cc_final: 0.8890 (mt) REVERT: A 396 ILE cc_start: 0.9237 (pt) cc_final: 0.8301 (mt) REVERT: A 464 ILE cc_start: 0.9337 (mt) cc_final: 0.9123 (mt) REVERT: A 618 CYS cc_start: 0.8818 (t) cc_final: 0.8346 (t) REVERT: B 168 PHE cc_start: 0.8833 (m-80) cc_final: 0.8429 (m-80) REVERT: B 176 PHE cc_start: 0.7459 (m-10) cc_final: 0.7108 (m-80) REVERT: B 194 VAL cc_start: 0.9074 (t) cc_final: 0.8841 (t) REVERT: B 219 ASP cc_start: 0.8187 (t0) cc_final: 0.7936 (t0) REVERT: B 289 LEU cc_start: 0.7798 (tp) cc_final: 0.7537 (tp) REVERT: B 411 SER cc_start: 0.5437 (m) cc_final: 0.5176 (m) REVERT: C 25 LEU cc_start: 0.9003 (mt) cc_final: 0.8802 (mp) REVERT: C 300 CYS cc_start: 0.9179 (m) cc_final: 0.8738 (m) REVERT: C 303 GLU cc_start: 0.8751 (mp0) cc_final: 0.8501 (mp0) REVERT: C 393 LEU cc_start: 0.9453 (mt) cc_final: 0.9237 (mt) REVERT: C 396 ILE cc_start: 0.9256 (pt) cc_final: 0.8421 (mt) REVERT: C 429 LEU cc_start: 0.9268 (mt) cc_final: 0.8917 (tp) REVERT: C 444 GLN cc_start: 0.9181 (tp40) cc_final: 0.8848 (tp40) REVERT: C 618 CYS cc_start: 0.9042 (t) cc_final: 0.8344 (t) REVERT: C 619 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8868 (tm-30) REVERT: C 626 LYS cc_start: 0.9250 (ttpt) cc_final: 0.9019 (ttpp) REVERT: C 703 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8319 (mt-10) REVERT: D 148 LEU cc_start: 0.8737 (mt) cc_final: 0.8306 (tt) REVERT: D 168 PHE cc_start: 0.8793 (m-80) cc_final: 0.8399 (m-80) REVERT: D 176 PHE cc_start: 0.7656 (m-10) cc_final: 0.7232 (m-80) REVERT: D 219 ASP cc_start: 0.8178 (t0) cc_final: 0.7929 (t0) REVERT: D 242 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8327 (ptm-80) REVERT: D 252 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8268 (ttp80) REVERT: D 260 LYS cc_start: 0.9212 (ttpp) cc_final: 0.8955 (ttpp) REVERT: D 286 GLU cc_start: 0.8120 (tt0) cc_final: 0.7495 (tt0) REVERT: D 289 LEU cc_start: 0.7718 (tp) cc_final: 0.7461 (tp) REVERT: D 427 LEU cc_start: 0.7201 (mp) cc_final: 0.6817 (mp) REVERT: E 291 ARG cc_start: 0.9482 (mtm110) cc_final: 0.9220 (mtm110) REVERT: E 295 HIS cc_start: 0.8862 (m-70) cc_final: 0.8603 (m90) REVERT: E 396 ILE cc_start: 0.9174 (pt) cc_final: 0.8253 (mt) REVERT: E 429 LEU cc_start: 0.9312 (mt) cc_final: 0.9084 (mm) REVERT: E 617 ASP cc_start: 0.8775 (m-30) cc_final: 0.8558 (m-30) REVERT: E 618 CYS cc_start: 0.8853 (t) cc_final: 0.8086 (t) REVERT: E 619 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8675 (tm-30) REVERT: F 139 VAL cc_start: 0.5829 (t) cc_final: 0.5582 (t) REVERT: F 155 ASP cc_start: 0.9204 (m-30) cc_final: 0.8775 (m-30) REVERT: F 198 VAL cc_start: 0.9369 (t) cc_final: 0.9145 (t) REVERT: F 219 ASP cc_start: 0.8220 (t70) cc_final: 0.7889 (t0) REVERT: F 259 ARG cc_start: 0.8611 (ptp-170) cc_final: 0.8213 (ttm170) REVERT: F 286 GLU cc_start: 0.8274 (tt0) cc_final: 0.7764 (mp0) REVERT: F 293 GLN cc_start: 0.7672 (tp40) cc_final: 0.7009 (tp40) REVERT: F 427 LEU cc_start: 0.6594 (mp) cc_final: 0.6194 (mp) REVERT: F 449 GLU cc_start: 0.6670 (tp30) cc_final: 0.6437 (tp30) REVERT: G 5 ILE cc_start: 0.7721 (mt) cc_final: 0.7419 (mt) REVERT: G 142 LEU cc_start: 0.8659 (tp) cc_final: 0.8419 (tp) REVERT: G 355 ILE cc_start: 0.8687 (mp) cc_final: 0.7328 (tp) REVERT: G 396 ILE cc_start: 0.9174 (pt) cc_final: 0.8397 (mt) REVERT: G 429 LEU cc_start: 0.9151 (mt) cc_final: 0.8694 (mm) REVERT: G 438 GLU cc_start: 0.8421 (tp30) cc_final: 0.8189 (tp30) REVERT: G 467 VAL cc_start: 0.9302 (t) cc_final: 0.9062 (t) REVERT: G 617 ASP cc_start: 0.8948 (m-30) cc_final: 0.8662 (m-30) REVERT: G 618 CYS cc_start: 0.9045 (t) cc_final: 0.8195 (p) REVERT: G 680 MET cc_start: 0.8011 (tmm) cc_final: 0.7728 (tmm) REVERT: G 684 ARG cc_start: 0.8416 (ptm160) cc_final: 0.8118 (ptm160) REVERT: G 703 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8342 (mt-10) REVERT: H 176 PHE cc_start: 0.7553 (m-10) cc_final: 0.6829 (m-10) REVERT: H 192 ASP cc_start: 0.8006 (m-30) cc_final: 0.7774 (m-30) REVERT: H 226 ARG cc_start: 0.8185 (tpt-90) cc_final: 0.7956 (tpt-90) REVERT: H 259 ARG cc_start: 0.8798 (ptp-170) cc_final: 0.8287 (ttp80) REVERT: H 289 LEU cc_start: 0.7711 (tp) cc_final: 0.7439 (tp) REVERT: I 228 ASP cc_start: 0.8901 (p0) cc_final: 0.8636 (p0) REVERT: I 355 ILE cc_start: 0.8893 (mp) cc_final: 0.8263 (mm) REVERT: I 393 LEU cc_start: 0.9403 (mt) cc_final: 0.9095 (mt) REVERT: I 394 THR cc_start: 0.9489 (p) cc_final: 0.9279 (p) REVERT: I 396 ILE cc_start: 0.9259 (pt) cc_final: 0.8496 (mt) REVERT: I 444 GLN cc_start: 0.9328 (mm-40) cc_final: 0.9098 (tm-30) REVERT: I 456 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8272 (mtp180) REVERT: I 618 CYS cc_start: 0.8917 (t) cc_final: 0.8196 (t) REVERT: I 619 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8844 (tm-30) REVERT: J 148 LEU cc_start: 0.8723 (mt) cc_final: 0.8290 (tp) REVERT: J 151 GLN cc_start: 0.8730 (mt0) cc_final: 0.8510 (tt0) REVERT: J 155 ASP cc_start: 0.9179 (m-30) cc_final: 0.8687 (m-30) REVERT: J 168 PHE cc_start: 0.8823 (m-80) cc_final: 0.8494 (m-80) REVERT: J 219 ASP cc_start: 0.8154 (t70) cc_final: 0.7779 (t0) REVERT: J 233 CYS cc_start: 0.7209 (t) cc_final: 0.6925 (t) REVERT: J 275 LEU cc_start: 0.7120 (mt) cc_final: 0.6905 (mp) REVERT: J 286 GLU cc_start: 0.8483 (tt0) cc_final: 0.7710 (tt0) REVERT: J 289 LEU cc_start: 0.8152 (tp) cc_final: 0.7951 (tp) REVERT: J 345 LEU cc_start: 0.6346 (mt) cc_final: 0.6094 (mt) REVERT: J 417 LEU cc_start: 0.8443 (tp) cc_final: 0.8221 (tp) REVERT: K 294 MET cc_start: 0.8754 (mmm) cc_final: 0.8542 (mmm) REVERT: K 295 HIS cc_start: 0.8855 (m-70) cc_final: 0.8590 (m-70) REVERT: K 355 ILE cc_start: 0.8676 (mp) cc_final: 0.7389 (tp) REVERT: K 396 ILE cc_start: 0.9166 (pt) cc_final: 0.8390 (mt) REVERT: K 426 GLU cc_start: 0.9003 (mp0) cc_final: 0.8769 (mp0) REVERT: K 439 MET cc_start: 0.8750 (mmm) cc_final: 0.8363 (mmm) REVERT: K 464 ILE cc_start: 0.9350 (mt) cc_final: 0.9128 (mt) REVERT: K 467 VAL cc_start: 0.9307 (t) cc_final: 0.9035 (t) REVERT: K 618 CYS cc_start: 0.9012 (t) cc_final: 0.8468 (p) REVERT: K 619 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8791 (tm-30) REVERT: K 626 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8898 (ttpp) REVERT: K 634 LYS cc_start: 0.9534 (ptmt) cc_final: 0.9110 (mmtm) REVERT: L 129 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6967 (tp30) REVERT: L 148 LEU cc_start: 0.8527 (mt) cc_final: 0.8217 (tt) REVERT: L 152 LEU cc_start: 0.8714 (mt) cc_final: 0.8309 (mt) REVERT: L 192 ASP cc_start: 0.7060 (m-30) cc_final: 0.6499 (m-30) REVERT: L 209 LEU cc_start: 0.8065 (tp) cc_final: 0.7839 (tp) REVERT: L 219 ASP cc_start: 0.8594 (t70) cc_final: 0.8077 (t70) REVERT: L 417 LEU cc_start: 0.8080 (tp) cc_final: 0.7740 (tp) REVERT: L 425 VAL cc_start: 0.8521 (t) cc_final: 0.8200 (p) REVERT: L 427 LEU cc_start: 0.7050 (mp) cc_final: 0.6178 (mp) REVERT: M 294 MET cc_start: 0.8992 (mmm) cc_final: 0.8747 (mmm) REVERT: M 336 LEU cc_start: 0.9196 (mt) cc_final: 0.8947 (mt) REVERT: M 355 ILE cc_start: 0.8578 (mp) cc_final: 0.7850 (mm) REVERT: M 438 GLU cc_start: 0.8438 (tp30) cc_final: 0.8206 (tp30) REVERT: M 444 GLN cc_start: 0.9340 (mm-40) cc_final: 0.8877 (tp40) REVERT: M 619 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8922 (tm-30) REVERT: M 638 ASP cc_start: 0.8121 (p0) cc_final: 0.7777 (p0) REVERT: M 642 LYS cc_start: 0.9454 (mttt) cc_final: 0.8769 (tttp) REVERT: N 139 VAL cc_start: 0.4719 (t) cc_final: 0.4438 (t) REVERT: N 148 LEU cc_start: 0.8528 (mt) cc_final: 0.8144 (tt) REVERT: N 168 PHE cc_start: 0.8543 (m-80) cc_final: 0.8293 (m-80) REVERT: N 176 PHE cc_start: 0.7542 (m-10) cc_final: 0.6528 (m-80) REVERT: N 219 ASP cc_start: 0.8521 (t0) cc_final: 0.8320 (t0) REVERT: N 268 TRP cc_start: 0.8450 (m100) cc_final: 0.8176 (m100) REVERT: N 286 GLU cc_start: 0.8559 (tt0) cc_final: 0.8333 (tt0) REVERT: N 289 LEU cc_start: 0.7875 (tp) cc_final: 0.7596 (tp) REVERT: N 427 LEU cc_start: 0.6797 (mp) cc_final: 0.6390 (mp) REVERT: O 110 GLU cc_start: 0.7390 (tt0) cc_final: 0.6941 (tt0) REVERT: O 131 HIS cc_start: 0.8301 (t70) cc_final: 0.7626 (t-90) REVERT: O 250 LEU cc_start: 0.9578 (mt) cc_final: 0.9271 (mt) REVERT: O 254 ASN cc_start: 0.8933 (m-40) cc_final: 0.8484 (t0) REVERT: O 355 ILE cc_start: 0.8653 (mp) cc_final: 0.7327 (tp) REVERT: O 383 PRO cc_start: 0.8625 (Cg_endo) cc_final: 0.8299 (Cg_exo) REVERT: O 396 ILE cc_start: 0.9123 (pt) cc_final: 0.8777 (tp) REVERT: O 617 ASP cc_start: 0.8913 (m-30) cc_final: 0.8711 (m-30) REVERT: O 618 CYS cc_start: 0.8891 (t) cc_final: 0.8248 (p) REVERT: O 619 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8726 (tm-30) REVERT: O 638 ASP cc_start: 0.8360 (p0) cc_final: 0.7955 (p0) REVERT: O 642 LYS cc_start: 0.9476 (mttt) cc_final: 0.8707 (tttt) REVERT: O 680 MET cc_start: 0.8374 (tmm) cc_final: 0.7956 (tmm) REVERT: P 148 LEU cc_start: 0.8417 (mt) cc_final: 0.8177 (mp) REVERT: P 176 PHE cc_start: 0.7803 (m-10) cc_final: 0.7403 (m-10) REVERT: P 192 ASP cc_start: 0.6673 (m-30) cc_final: 0.6422 (m-30) REVERT: P 219 ASP cc_start: 0.8686 (t70) cc_final: 0.8462 (t0) REVERT: P 229 GLN cc_start: 0.8956 (mt0) cc_final: 0.8736 (tt0) REVERT: P 289 LEU cc_start: 0.7616 (tp) cc_final: 0.7397 (tp) REVERT: P 449 GLU cc_start: 0.6284 (tp30) cc_final: 0.6002 (tp30) outliers start: 2 outliers final: 0 residues processed: 3006 average time/residue: 1.4032 time to fit residues: 6835.4171 Evaluate side-chains 2608 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2608 time to evaluate : 5.906 ------------------------------------------------------------------------------- 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: 2.9990 chunk 550 optimal weight: 5.9990 chunk 450 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 662 optimal weight: 5.9990 chunk 715 optimal weight: 10.0000 chunk 589 optimal weight: 0.9990 chunk 656 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 531 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN A 708 HIS B 348 HIS B 414 GLN C 27 GLN C 249 GLN C 420 GLN E 27 GLN ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 635 ASN E 708 HIS G 27 GLN G 249 GLN G 708 HIS I 27 GLN I 95 HIS I 249 GLN ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** K 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 270 GLN K 420 GLN K 708 HIS M 249 GLN M 270 GLN ** M 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 95 HIS ** O 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 GLN ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 58944 Z= 0.331 Angle : 0.655 7.600 80072 Z= 0.370 Chirality : 0.039 0.162 9440 Planarity : 0.008 0.079 10304 Dihedral : 6.478 57.805 8248 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.10 % Favored : 94.51 % Rotamer: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % 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: -0.64 (0.09), residues: 7288 helix: 0.04 (0.07), residues: 4128 sheet: -1.50 (0.19), residues: 600 loop : -0.68 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 268 HIS 0.011 0.002 HIS B 348 PHE 0.019 0.002 PHE C 93 TYR 0.021 0.002 TYR G 449 ARG 0.007 0.001 ARG G 263 *********************** 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: 2 poor density : 2825 time to evaluate : 6.568 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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8154 (m-80) cc_final: 0.6643 (m-80) REVERT: A 110 GLU cc_start: 0.8447 (tt0) cc_final: 0.7625 (tt0) REVERT: A 294 MET cc_start: 0.8859 (mmm) cc_final: 0.8560 (mmm) REVERT: A 336 LEU cc_start: 0.9257 (mt) cc_final: 0.9015 (mt) REVERT: A 425 GLU cc_start: 0.8384 (pp20) cc_final: 0.8159 (tm-30) REVERT: A 444 GLN cc_start: 0.8919 (tp40) cc_final: 0.8569 (tm-30) REVERT: A 466 GLU cc_start: 0.9053 (pp20) cc_final: 0.8539 (pp20) REVERT: A 467 VAL cc_start: 0.9303 (t) cc_final: 0.9070 (t) REVERT: A 618 CYS cc_start: 0.9019 (t) cc_final: 0.8647 (t) REVERT: A 619 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8714 (tm-30) REVERT: B 219 ASP cc_start: 0.8160 (t0) cc_final: 0.7883 (t0) REVERT: B 289 LEU cc_start: 0.7659 (tp) cc_final: 0.7388 (tp) REVERT: B 345 LEU cc_start: 0.5037 (mt) cc_final: 0.4708 (mt) REVERT: C 93 PHE cc_start: 0.8263 (m-10) cc_final: 0.7402 (m-10) REVERT: C 173 PHE cc_start: 0.8784 (m-80) cc_final: 0.8364 (m-80) REVERT: C 268 PHE cc_start: 0.9226 (t80) cc_final: 0.8977 (t80) REVERT: C 294 MET cc_start: 0.9154 (mmm) cc_final: 0.8904 (mmm) REVERT: C 300 CYS cc_start: 0.9245 (m) cc_final: 0.8772 (m) REVERT: C 303 GLU cc_start: 0.8764 (mp0) cc_final: 0.8496 (mp0) REVERT: C 396 ILE cc_start: 0.9349 (pt) cc_final: 0.9123 (tp) REVERT: C 444 GLN cc_start: 0.9265 (tp40) cc_final: 0.8830 (tm-30) REVERT: C 619 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8900 (tm-30) REVERT: C 626 LYS cc_start: 0.9320 (ttpt) cc_final: 0.9107 (ttpp) REVERT: C 630 LEU cc_start: 0.9552 (mt) cc_final: 0.9347 (mt) REVERT: C 680 MET cc_start: 0.8343 (tmm) cc_final: 0.8070 (tmm) REVERT: C 703 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8249 (mt-10) REVERT: D 219 ASP cc_start: 0.8188 (t0) cc_final: 0.7973 (t0) REVERT: D 242 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8391 (ptp-170) REVERT: D 260 LYS cc_start: 0.9313 (ttpp) cc_final: 0.8905 (ttpp) REVERT: D 289 LEU cc_start: 0.7659 (tp) cc_final: 0.7358 (tp) REVERT: E 24 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8984 (mp10) REVERT: E 150 MET cc_start: 0.7858 (tpt) cc_final: 0.7221 (tpt) REVERT: E 173 PHE cc_start: 0.8581 (m-80) cc_final: 0.8350 (m-80) REVERT: E 291 ARG cc_start: 0.9496 (mtm110) cc_final: 0.9271 (mtm110) REVERT: E 294 MET cc_start: 0.8796 (mmm) cc_final: 0.8551 (mmm) REVERT: E 295 HIS cc_start: 0.8850 (m-70) cc_final: 0.8570 (m-70) REVERT: E 336 LEU cc_start: 0.9192 (mt) cc_final: 0.8945 (mt) REVERT: E 426 GLU cc_start: 0.8605 (mp0) cc_final: 0.8350 (mp0) REVERT: E 467 VAL cc_start: 0.9341 (t) cc_final: 0.9116 (t) REVERT: E 619 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8699 (tm-30) REVERT: E 634 LYS cc_start: 0.9466 (ptmt) cc_final: 0.8940 (mmtm) REVERT: F 155 ASP cc_start: 0.9131 (m-30) cc_final: 0.8931 (m-30) REVERT: F 176 PHE cc_start: 0.7888 (m-10) cc_final: 0.7645 (m-10) REVERT: F 219 ASP cc_start: 0.8220 (t70) cc_final: 0.7877 (t0) REVERT: F 259 ARG cc_start: 0.8683 (ptp-170) cc_final: 0.8445 (ttm170) REVERT: F 286 GLU cc_start: 0.8189 (tt0) cc_final: 0.7839 (mp0) REVERT: F 289 LEU cc_start: 0.7939 (tp) cc_final: 0.7683 (tp) REVERT: F 293 GLN cc_start: 0.7342 (tp40) cc_final: 0.6965 (tp40) REVERT: F 427 LEU cc_start: 0.7161 (mp) cc_final: 0.6458 (mp) REVERT: G 110 GLU cc_start: 0.7607 (tt0) cc_final: 0.7387 (tt0) REVERT: G 173 PHE cc_start: 0.8700 (m-80) cc_final: 0.8462 (m-80) REVERT: G 291 ARG cc_start: 0.9364 (ttp-110) cc_final: 0.9152 (ttp-110) REVERT: G 294 MET cc_start: 0.8822 (mmm) cc_final: 0.8605 (mmm) REVERT: G 295 HIS cc_start: 0.8809 (m-70) cc_final: 0.8575 (m-70) REVERT: G 303 GLU cc_start: 0.8882 (mp0) cc_final: 0.8607 (mp0) REVERT: G 618 CYS cc_start: 0.9160 (t) cc_final: 0.8364 (t) REVERT: G 649 VAL cc_start: 0.9250 (t) cc_final: 0.9023 (t) REVERT: G 680 MET cc_start: 0.8087 (tmm) cc_final: 0.7670 (tmm) REVERT: H 176 PHE cc_start: 0.7701 (m-10) cc_final: 0.7348 (m-80) REVERT: H 192 ASP cc_start: 0.8111 (m-30) cc_final: 0.7847 (m-30) REVERT: H 209 LEU cc_start: 0.8009 (tp) cc_final: 0.7731 (tp) REVERT: H 219 ASP cc_start: 0.8522 (t0) cc_final: 0.8278 (t0) REVERT: H 289 LEU cc_start: 0.7623 (tp) cc_final: 0.7374 (tp) REVERT: I 93 PHE cc_start: 0.8446 (m-10) cc_final: 0.7630 (m-10) REVERT: I 173 PHE cc_start: 0.8605 (m-80) cc_final: 0.8365 (m-80) REVERT: I 228 ASP cc_start: 0.8873 (p0) cc_final: 0.8590 (p0) REVERT: I 287 ARG cc_start: 0.9232 (mmt180) cc_final: 0.9031 (mmt180) REVERT: I 336 LEU cc_start: 0.9372 (mt) cc_final: 0.9117 (mt) REVERT: I 393 LEU cc_start: 0.9475 (mt) cc_final: 0.9169 (mt) REVERT: I 396 ILE cc_start: 0.9312 (pt) cc_final: 0.8635 (mt) REVERT: I 618 CYS cc_start: 0.9116 (t) cc_final: 0.8607 (t) REVERT: I 619 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8903 (tm-30) REVERT: I 680 MET cc_start: 0.8213 (tmm) cc_final: 0.7929 (tmm) REVERT: J 148 LEU cc_start: 0.8940 (mt) cc_final: 0.8532 (tp) REVERT: J 151 GLN cc_start: 0.8715 (mt0) cc_final: 0.8474 (tt0) REVERT: J 159 GLU cc_start: 0.9440 (mm-30) cc_final: 0.8969 (mt-10) REVERT: J 168 PHE cc_start: 0.8866 (m-80) cc_final: 0.8511 (m-80) REVERT: J 219 ASP cc_start: 0.8076 (t70) cc_final: 0.7679 (t0) REVERT: J 242 ARG cc_start: 0.8930 (ptm160) cc_final: 0.8592 (ptm-80) REVERT: J 289 LEU cc_start: 0.7854 (tp) cc_final: 0.7648 (tp) REVERT: K 139 VAL cc_start: 0.9643 (m) cc_final: 0.9308 (p) REVERT: K 287 ARG cc_start: 0.8989 (mmt180) cc_final: 0.8573 (mmp-170) REVERT: K 291 ARG cc_start: 0.9469 (mtm110) cc_final: 0.9263 (mtp-110) REVERT: K 294 MET cc_start: 0.8798 (mmm) cc_final: 0.8592 (mmm) REVERT: K 295 HIS cc_start: 0.8824 (m-70) cc_final: 0.8576 (m90) REVERT: K 355 ILE cc_start: 0.8742 (mp) cc_final: 0.8049 (mm) REVERT: K 396 ILE cc_start: 0.9257 (pt) cc_final: 0.8991 (tp) REVERT: K 464 ILE cc_start: 0.9352 (mt) cc_final: 0.9136 (mt) REVERT: K 486 LEU cc_start: 0.9316 (mt) cc_final: 0.9086 (mm) REVERT: K 617 ASP cc_start: 0.8496 (m-30) cc_final: 0.8283 (m-30) REVERT: K 626 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8897 (ttpp) REVERT: K 634 LYS cc_start: 0.9536 (ptmt) cc_final: 0.9119 (mmtm) REVERT: K 680 MET cc_start: 0.8309 (tmm) cc_final: 0.7902 (tmm) REVERT: L 129 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7029 (tp30) REVERT: L 148 LEU cc_start: 0.8570 (mt) cc_final: 0.8175 (tt) REVERT: L 159 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8497 (mt-10) REVERT: L 176 PHE cc_start: 0.7064 (m-10) cc_final: 0.6731 (m-10) REVERT: L 219 ASP cc_start: 0.8529 (t70) cc_final: 0.8285 (t0) REVERT: L 289 LEU cc_start: 0.7758 (tp) cc_final: 0.7464 (tp) REVERT: L 293 GLN cc_start: 0.7546 (tp40) cc_final: 0.7342 (tp-100) REVERT: L 427 LEU cc_start: 0.7575 (mp) cc_final: 0.7300 (mp) REVERT: M 15 PHE cc_start: 0.9196 (m-80) cc_final: 0.8920 (m-80) REVERT: M 24 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8884 (mp10) REVERT: M 139 VAL cc_start: 0.9595 (m) cc_final: 0.9341 (p) REVERT: M 140 VAL cc_start: 0.9574 (t) cc_final: 0.9332 (p) REVERT: M 336 LEU cc_start: 0.9232 (mt) cc_final: 0.8956 (mt) REVERT: M 355 ILE cc_start: 0.8774 (mp) cc_final: 0.8073 (mm) REVERT: M 393 LEU cc_start: 0.9527 (mt) cc_final: 0.9265 (mt) REVERT: M 396 ILE cc_start: 0.9234 (pt) cc_final: 0.8419 (mt) REVERT: M 444 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9130 (tm-30) REVERT: M 466 GLU cc_start: 0.9020 (pp20) cc_final: 0.8812 (pp20) REVERT: M 619 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8913 (tm-30) REVERT: M 638 ASP cc_start: 0.8056 (p0) cc_final: 0.7727 (p0) REVERT: M 642 LYS cc_start: 0.9453 (mttt) cc_final: 0.8760 (tttp) REVERT: N 148 LEU cc_start: 0.8595 (mt) cc_final: 0.8265 (tp) REVERT: N 152 LEU cc_start: 0.8521 (mt) cc_final: 0.8138 (mt) REVERT: N 168 PHE cc_start: 0.8631 (m-80) cc_final: 0.8308 (m-80) REVERT: N 268 TRP cc_start: 0.8580 (m100) cc_final: 0.8368 (m100) REVERT: N 289 LEU cc_start: 0.7677 (tp) cc_final: 0.7376 (tp) REVERT: O 15 PHE cc_start: 0.8989 (m-80) cc_final: 0.8674 (m-80) REVERT: O 122 ASN cc_start: 0.8976 (t0) cc_final: 0.8047 (t0) REVERT: O 336 LEU cc_start: 0.9224 (mt) cc_final: 0.8937 (mt) REVERT: O 383 PRO cc_start: 0.8970 (Cg_endo) cc_final: 0.8685 (Cg_exo) REVERT: O 456 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7164 (ttm170) REVERT: O 464 ILE cc_start: 0.9464 (mt) cc_final: 0.9191 (mt) REVERT: O 466 GLU cc_start: 0.8963 (pp20) cc_final: 0.8210 (pp20) REVERT: O 467 VAL cc_start: 0.9276 (m) cc_final: 0.8826 (m) REVERT: O 470 CYS cc_start: 0.8190 (m) cc_final: 0.7965 (m) REVERT: O 618 CYS cc_start: 0.8864 (t) cc_final: 0.8348 (p) REVERT: O 619 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8778 (tm-30) REVERT: O 634 LYS cc_start: 0.9451 (ptmt) cc_final: 0.9100 (mmtm) REVERT: O 638 ASP cc_start: 0.8373 (p0) cc_final: 0.7975 (p0) REVERT: O 642 LYS cc_start: 0.9482 (mttt) cc_final: 0.8701 (tttt) REVERT: P 176 PHE cc_start: 0.7859 (m-10) cc_final: 0.6955 (m-10) REVERT: P 229 GLN cc_start: 0.9096 (mt0) cc_final: 0.8737 (tt0) REVERT: P 289 LEU cc_start: 0.7509 (tp) cc_final: 0.7307 (tp) REVERT: P 293 GLN cc_start: 0.7732 (tt0) cc_final: 0.6761 (tp-100) outliers start: 2 outliers final: 2 residues processed: 2825 average time/residue: 1.3888 time to fit residues: 6359.4908 Evaluate side-chains 2547 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2545 time to evaluate : 6.436 ------------------------------------------------------------------------------- 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: 9.9990 chunk 497 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 9.9990 chunk 664 optimal weight: 0.7980 chunk 703 optimal weight: 0.7980 chunk 347 optimal weight: 9.9990 chunk 629 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 187 GLN B 348 HIS C 95 HIS C 708 HIS ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 HIS ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 GLN K 9 ASN K 95 HIS K 249 GLN M 420 GLN O 249 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 58944 Z= 0.180 Angle : 0.531 7.612 80072 Z= 0.288 Chirality : 0.039 0.395 9440 Planarity : 0.006 0.071 10304 Dihedral : 6.216 57.399 8248 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.86 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.11 (0.10), residues: 7288 helix: 0.73 (0.08), residues: 4088 sheet: -1.49 (0.20), residues: 584 loop : -0.43 (0.13), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 268 HIS 0.011 0.001 HIS B 348 PHE 0.015 0.001 PHE O 370 TYR 0.013 0.001 TYR I 101 ARG 0.007 0.000 ARG A 441 *********************** 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 2853 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2853 time to evaluate : 6.476 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: 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8251 (tt0) cc_final: 0.7913 (tt0) REVERT: A 173 PHE cc_start: 0.8731 (m-80) cc_final: 0.8487 (m-80) REVERT: A 220 MET cc_start: 0.6122 (tmm) cc_final: 0.5897 (ppp) REVERT: A 287 ARG cc_start: 0.9006 (mmt180) cc_final: 0.8610 (mmm160) REVERT: A 294 MET cc_start: 0.8828 (mmm) cc_final: 0.8498 (mmm) REVERT: A 336 LEU cc_start: 0.9220 (mt) cc_final: 0.8873 (mt) REVERT: A 355 ILE cc_start: 0.8601 (mp) cc_final: 0.7568 (tp) REVERT: A 396 ILE cc_start: 0.9303 (pt) cc_final: 0.8925 (tp) REVERT: A 425 GLU cc_start: 0.8296 (pp20) cc_final: 0.8045 (tm-30) REVERT: A 444 GLN cc_start: 0.9001 (tp40) cc_final: 0.8583 (tm-30) REVERT: A 466 GLU cc_start: 0.8922 (pp20) cc_final: 0.8073 (pp20) REVERT: A 618 CYS cc_start: 0.8902 (t) cc_final: 0.8629 (t) REVERT: A 619 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8712 (tm-30) REVERT: A 680 MET cc_start: 0.7787 (tmm) cc_final: 0.7416 (tmm) REVERT: B 159 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8756 (mt-10) REVERT: B 176 PHE cc_start: 0.7295 (m-10) cc_final: 0.7039 (m-80) REVERT: B 219 ASP cc_start: 0.8194 (t0) cc_final: 0.7889 (t0) REVERT: B 268 TRP cc_start: 0.8015 (m100) cc_final: 0.7348 (m100) REVERT: B 289 LEU cc_start: 0.7497 (tp) cc_final: 0.7274 (tp) REVERT: B 345 LEU cc_start: 0.5134 (mt) cc_final: 0.4765 (mt) REVERT: C 15 PHE cc_start: 0.9072 (m-80) cc_final: 0.8788 (m-80) REVERT: C 173 PHE cc_start: 0.8756 (m-80) cc_final: 0.8360 (m-80) REVERT: C 176 ASN cc_start: 0.8897 (t0) cc_final: 0.8503 (t0) REVERT: C 178 ASN cc_start: 0.8210 (t0) cc_final: 0.7730 (t0) REVERT: C 268 PHE cc_start: 0.9153 (t80) cc_final: 0.8931 (t80) REVERT: C 294 MET cc_start: 0.9075 (mmm) cc_final: 0.8807 (mmm) REVERT: C 300 CYS cc_start: 0.9197 (m) cc_final: 0.8722 (m) REVERT: C 303 GLU cc_start: 0.8699 (mp0) cc_final: 0.8410 (mp0) REVERT: C 336 LEU cc_start: 0.9167 (mt) cc_final: 0.8941 (mt) REVERT: C 426 GLU cc_start: 0.8861 (mp0) cc_final: 0.8539 (mp0) REVERT: C 429 LEU cc_start: 0.9391 (mp) cc_final: 0.9130 (mm) REVERT: C 444 GLN cc_start: 0.9256 (tp40) cc_final: 0.8769 (tm-30) REVERT: C 448 ASN cc_start: 0.9013 (m-40) cc_final: 0.8671 (m110) REVERT: C 466 GLU cc_start: 0.9052 (pp20) cc_final: 0.8153 (pp20) REVERT: C 485 ASN cc_start: 0.8832 (m110) cc_final: 0.8601 (m110) REVERT: C 619 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8846 (tm-30) REVERT: C 626 LYS cc_start: 0.9278 (ttpt) cc_final: 0.9073 (ttpp) REVERT: D 148 LEU cc_start: 0.8481 (mp) cc_final: 0.8009 (tt) REVERT: D 176 PHE cc_start: 0.7727 (m-10) cc_final: 0.7262 (m-80) REVERT: D 219 ASP cc_start: 0.8171 (t0) cc_final: 0.7919 (t0) REVERT: D 252 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8396 (ttp80) REVERT: D 289 LEU cc_start: 0.7673 (tp) cc_final: 0.7403 (tp) REVERT: E 24 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8974 (mp10) REVERT: E 150 MET cc_start: 0.7493 (tpt) cc_final: 0.7042 (tpt) REVERT: E 173 PHE cc_start: 0.8590 (m-80) cc_final: 0.8360 (m-80) REVERT: E 250 LEU cc_start: 0.9677 (mt) cc_final: 0.9330 (mt) REVERT: E 291 ARG cc_start: 0.9485 (mtm110) cc_final: 0.9169 (mtm110) REVERT: E 295 HIS cc_start: 0.8852 (m-70) cc_final: 0.8591 (m90) REVERT: E 336 LEU cc_start: 0.9150 (mt) cc_final: 0.8924 (mt) REVERT: E 396 ILE cc_start: 0.9248 (pt) cc_final: 0.8976 (tp) REVERT: E 426 GLU cc_start: 0.8456 (mp0) cc_final: 0.8060 (mp0) REVERT: E 466 GLU cc_start: 0.8940 (pp20) cc_final: 0.8015 (pp20) REVERT: E 619 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8653 (tm-30) REVERT: E 634 LYS cc_start: 0.9448 (ptmt) cc_final: 0.8922 (mmtm) REVERT: F 129 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7168 (tp30) REVERT: F 159 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8648 (mt-10) REVERT: F 176 PHE cc_start: 0.7832 (m-10) cc_final: 0.7505 (m-10) REVERT: F 206 LEU cc_start: 0.8410 (mm) cc_final: 0.7642 (mm) REVERT: F 219 ASP cc_start: 0.8177 (t70) cc_final: 0.7839 (t0) REVERT: F 233 CYS cc_start: 0.8081 (t) cc_final: 0.7479 (p) REVERT: F 268 TRP cc_start: 0.7863 (m100) cc_final: 0.7343 (m100) REVERT: F 292 VAL cc_start: 0.7265 (t) cc_final: 0.7035 (t) REVERT: F 293 GLN cc_start: 0.7229 (tp40) cc_final: 0.6980 (tp-100) REVERT: F 367 CYS cc_start: 0.7588 (m) cc_final: 0.7379 (m) REVERT: G 89 GLU cc_start: 0.7813 (mp0) cc_final: 0.7608 (mp0) REVERT: G 173 PHE cc_start: 0.8646 (m-80) cc_final: 0.8417 (m-80) REVERT: G 287 ARG cc_start: 0.9048 (mmt180) cc_final: 0.8475 (mmp-170) REVERT: G 303 GLU cc_start: 0.8874 (mp0) cc_final: 0.8619 (mp0) REVERT: G 355 ILE cc_start: 0.8716 (mp) cc_final: 0.8143 (mm) REVERT: G 396 ILE cc_start: 0.9160 (pt) cc_final: 0.8761 (tp) REVERT: G 466 GLU cc_start: 0.9091 (pp20) cc_final: 0.8176 (pp20) REVERT: G 467 VAL cc_start: 0.9296 (t) cc_final: 0.8965 (t) REVERT: G 470 CYS cc_start: 0.8322 (m) cc_final: 0.8047 (m) REVERT: G 618 CYS cc_start: 0.9109 (t) cc_final: 0.8299 (t) REVERT: G 626 LYS cc_start: 0.9210 (ttpp) cc_final: 0.8904 (ttpp) REVERT: G 634 LYS cc_start: 0.9395 (pttt) cc_final: 0.8920 (mmtm) REVERT: G 680 MET cc_start: 0.8038 (tmm) cc_final: 0.7641 (tmm) REVERT: H 129 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7206 (tp30) REVERT: H 176 PHE cc_start: 0.7670 (m-10) cc_final: 0.7366 (m-80) REVERT: H 219 ASP cc_start: 0.8485 (t0) cc_final: 0.8247 (t0) REVERT: H 259 ARG cc_start: 0.8660 (ptp-170) cc_final: 0.8378 (ttp80) REVERT: H 289 LEU cc_start: 0.7639 (tp) cc_final: 0.7381 (tp) REVERT: H 422 ASN cc_start: 0.7270 (t0) cc_final: 0.7007 (t0) REVERT: I 4 LEU cc_start: 0.9506 (mt) cc_final: 0.9200 (mt) REVERT: I 15 PHE cc_start: 0.9005 (m-80) cc_final: 0.8796 (m-80) REVERT: I 93 PHE cc_start: 0.7552 (m-10) cc_final: 0.7321 (m-10) REVERT: I 173 PHE cc_start: 0.8555 (m-80) cc_final: 0.8350 (m-80) REVERT: I 228 ASP cc_start: 0.8852 (p0) cc_final: 0.8567 (p0) REVERT: I 336 LEU cc_start: 0.9279 (mt) cc_final: 0.9016 (mt) REVERT: I 393 LEU cc_start: 0.9453 (mt) cc_final: 0.9126 (mt) REVERT: I 396 ILE cc_start: 0.9279 (pt) cc_final: 0.8570 (mt) REVERT: I 466 GLU cc_start: 0.9037 (pp20) cc_final: 0.8439 (pp20) REVERT: I 618 CYS cc_start: 0.9038 (t) cc_final: 0.8565 (t) REVERT: I 619 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8885 (tm-30) REVERT: I 676 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5869 (mt-10) REVERT: I 703 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8124 (mt-10) REVERT: J 148 LEU cc_start: 0.8717 (mt) cc_final: 0.8278 (tp) REVERT: J 168 PHE cc_start: 0.8846 (m-80) cc_final: 0.8567 (m-80) REVERT: J 219 ASP cc_start: 0.8078 (t70) cc_final: 0.7725 (t0) REVERT: J 289 LEU cc_start: 0.7846 (tp) cc_final: 0.7607 (tp) REVERT: J 367 CYS cc_start: 0.7616 (m) cc_final: 0.7397 (m) REVERT: J 427 LEU cc_start: 0.7274 (mp) cc_final: 0.7037 (mp) REVERT: K 89 GLU cc_start: 0.7930 (mp0) cc_final: 0.7692 (mp0) REVERT: K 139 VAL cc_start: 0.9674 (m) cc_final: 0.9333 (p) REVERT: K 295 HIS cc_start: 0.8802 (m-70) cc_final: 0.8542 (m90) REVERT: K 393 LEU cc_start: 0.9590 (mt) cc_final: 0.9375 (mt) REVERT: K 396 ILE cc_start: 0.9261 (pt) cc_final: 0.8614 (mt) REVERT: K 439 MET cc_start: 0.8677 (mmm) cc_final: 0.8220 (mmm) REVERT: K 464 ILE cc_start: 0.9334 (mt) cc_final: 0.9119 (mt) REVERT: K 466 GLU cc_start: 0.9035 (pp20) cc_final: 0.8073 (pp20) REVERT: K 470 CYS cc_start: 0.8110 (m) cc_final: 0.7898 (m) REVERT: K 617 ASP cc_start: 0.8436 (m-30) cc_final: 0.8231 (m-30) REVERT: K 634 LYS cc_start: 0.9513 (ptmt) cc_final: 0.9089 (mmtm) REVERT: K 680 MET cc_start: 0.8322 (tmm) cc_final: 0.7753 (tmm) REVERT: K 710 TRP cc_start: 0.3632 (t-100) cc_final: 0.3353 (t-100) REVERT: L 129 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6983 (tp30) REVERT: L 152 LEU cc_start: 0.8624 (mt) cc_final: 0.8405 (mt) REVERT: L 159 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8506 (mt-10) REVERT: L 176 PHE cc_start: 0.6879 (m-10) cc_final: 0.6655 (m-10) REVERT: L 219 ASP cc_start: 0.8473 (t70) cc_final: 0.8119 (t0) REVERT: L 289 LEU cc_start: 0.7614 (tp) cc_final: 0.7292 (tp) REVERT: L 422 ASN cc_start: 0.6656 (t0) cc_final: 0.6399 (t0) REVERT: M 15 PHE cc_start: 0.9119 (m-80) cc_final: 0.8809 (m-80) REVERT: M 24 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8802 (mp10) REVERT: M 139 VAL cc_start: 0.9568 (m) cc_final: 0.9324 (p) REVERT: M 287 ARG cc_start: 0.9071 (mmt180) cc_final: 0.8662 (mmm160) REVERT: M 393 LEU cc_start: 0.9489 (mt) cc_final: 0.9210 (mt) REVERT: M 396 ILE cc_start: 0.9212 (pt) cc_final: 0.8395 (mt) REVERT: M 425 GLU cc_start: 0.8331 (pp20) cc_final: 0.8050 (tm-30) REVERT: M 466 GLU cc_start: 0.8980 (pp20) cc_final: 0.8674 (pp20) REVERT: M 619 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8925 (tm-30) REVERT: M 638 ASP cc_start: 0.7790 (p0) cc_final: 0.7481 (p0) REVERT: M 642 LYS cc_start: 0.9339 (mttt) cc_final: 0.8568 (tttt) REVERT: N 168 PHE cc_start: 0.8647 (m-80) cc_final: 0.8335 (m-80) REVERT: N 219 ASP cc_start: 0.8644 (t70) cc_final: 0.8386 (t0) REVERT: N 266 VAL cc_start: 0.9050 (t) cc_final: 0.8297 (t) REVERT: N 268 TRP cc_start: 0.8555 (m100) cc_final: 0.8304 (m100) REVERT: N 289 LEU cc_start: 0.7672 (tp) cc_final: 0.7331 (tp) REVERT: O 15 PHE cc_start: 0.8891 (m-80) cc_final: 0.8506 (m-80) REVERT: O 110 GLU cc_start: 0.7650 (tt0) cc_final: 0.7150 (tt0) REVERT: O 122 ASN cc_start: 0.8716 (t0) cc_final: 0.8363 (t0) REVERT: O 294 MET cc_start: 0.9109 (mmp) cc_final: 0.8572 (mmm) REVERT: O 336 LEU cc_start: 0.9187 (mt) cc_final: 0.8882 (mt) REVERT: O 426 GLU cc_start: 0.8209 (mp0) cc_final: 0.7837 (mp0) REVERT: O 429 LEU cc_start: 0.9364 (mt) cc_final: 0.9092 (mm) REVERT: O 460 LEU cc_start: 0.9270 (tp) cc_final: 0.9064 (tp) REVERT: O 464 ILE cc_start: 0.9479 (mt) cc_final: 0.9219 (mt) REVERT: O 466 GLU cc_start: 0.8910 (pp20) cc_final: 0.8319 (pp20) REVERT: O 467 VAL cc_start: 0.9133 (m) cc_final: 0.8682 (m) REVERT: O 473 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8338 (ttm-80) REVERT: O 618 CYS cc_start: 0.8788 (t) cc_final: 0.8333 (p) REVERT: O 619 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8753 (tm-30) REVERT: O 626 LYS cc_start: 0.9014 (ttpp) cc_final: 0.8798 (ttpp) REVERT: O 634 LYS cc_start: 0.9435 (ptmt) cc_final: 0.9080 (mmtm) REVERT: O 638 ASP cc_start: 0.8035 (p0) cc_final: 0.7739 (p0) REVERT: O 642 LYS cc_start: 0.9340 (mttt) cc_final: 0.8524 (tttt) REVERT: P 163 TYR cc_start: 0.8370 (m-10) cc_final: 0.7780 (m-10) REVERT: P 176 PHE cc_start: 0.7444 (m-10) cc_final: 0.6885 (m-10) REVERT: P 229 GLN cc_start: 0.9073 (mt0) cc_final: 0.8703 (tt0) REVERT: P 317 LEU cc_start: 0.7020 (mm) cc_final: 0.6788 (mp) REVERT: P 422 ASN cc_start: 0.7023 (t0) cc_final: 0.6747 (t0) REVERT: P 427 LEU cc_start: 0.7577 (mp) cc_final: 0.7307 (mp) outliers start: 0 outliers final: 0 residues processed: 2853 average time/residue: 1.4378 time to fit residues: 6706.2210 Evaluate side-chains 2581 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2581 time to evaluate : 6.463 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 8.9990 chunk 523 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 chunk 600 optimal weight: 1.9990 chunk 486 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 631 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 348 HIS ** C 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 635 ASN ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 708 HIS N 161 GLN O 254 ASN O 270 GLN ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 708 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 58944 Z= 0.264 Angle : 0.589 8.263 80072 Z= 0.326 Chirality : 0.039 0.354 9440 Planarity : 0.006 0.064 10304 Dihedral : 6.119 56.609 8248 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.80 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.10 (0.10), residues: 7288 helix: 0.64 (0.08), residues: 4048 sheet: -1.55 (0.20), residues: 584 loop : -0.67 (0.13), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 268 HIS 0.010 0.001 HIS B 348 PHE 0.020 0.002 PHE C 93 TYR 0.019 0.002 TYR A 493 ARG 0.008 0.001 ARG M 423 *********************** 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 2743 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2743 time to evaluate : 6.515 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: 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.8948 (m-80) cc_final: 0.8580 (m-80) REVERT: A 110 GLU cc_start: 0.8373 (tt0) cc_final: 0.8035 (tt0) REVERT: A 173 PHE cc_start: 0.8705 (m-80) cc_final: 0.8492 (m-80) REVERT: A 294 MET cc_start: 0.8948 (mmm) cc_final: 0.8556 (mmm) REVERT: A 336 LEU cc_start: 0.9260 (mt) cc_final: 0.8988 (mt) REVERT: A 361 CYS cc_start: 0.6073 (p) cc_final: 0.5827 (p) REVERT: A 398 ASN cc_start: 0.8749 (m110) cc_final: 0.8537 (m110) REVERT: A 444 GLN cc_start: 0.9144 (tp40) cc_final: 0.8744 (tm-30) REVERT: A 466 GLU cc_start: 0.8937 (pp20) cc_final: 0.8110 (pp20) REVERT: A 470 CYS cc_start: 0.8297 (m) cc_final: 0.8085 (m) REVERT: A 618 CYS cc_start: 0.8953 (t) cc_final: 0.8686 (t) REVERT: A 619 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8712 (tm-30) REVERT: B 155 ASP cc_start: 0.8985 (m-30) cc_final: 0.8710 (m-30) REVERT: B 176 PHE cc_start: 0.7638 (m-10) cc_final: 0.7327 (m-80) REVERT: B 219 ASP cc_start: 0.8183 (t0) cc_final: 0.7882 (t0) REVERT: B 277 CYS cc_start: 0.8474 (p) cc_final: 0.7618 (p) REVERT: B 289 LEU cc_start: 0.7394 (tp) cc_final: 0.7152 (tp) REVERT: B 293 GLN cc_start: 0.6988 (tt0) cc_final: 0.6188 (tp-100) REVERT: C 89 GLU cc_start: 0.7527 (mp0) cc_final: 0.7048 (mp0) REVERT: C 173 PHE cc_start: 0.8886 (m-80) cc_final: 0.8553 (m-80) REVERT: C 268 PHE cc_start: 0.9233 (t80) cc_final: 0.9004 (t80) REVERT: C 294 MET cc_start: 0.9137 (mmm) cc_final: 0.8897 (mmm) REVERT: C 300 CYS cc_start: 0.9190 (m) cc_final: 0.8666 (m) REVERT: C 303 GLU cc_start: 0.8712 (mp0) cc_final: 0.8473 (mp0) REVERT: C 336 LEU cc_start: 0.9289 (mt) cc_final: 0.9054 (mt) REVERT: C 396 ILE cc_start: 0.9362 (pt) cc_final: 0.9140 (tp) REVERT: C 444 GLN cc_start: 0.9288 (tp40) cc_final: 0.8810 (tm-30) REVERT: C 466 GLU cc_start: 0.9059 (pp20) cc_final: 0.8437 (pp20) REVERT: C 619 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8848 (tm-30) REVERT: C 630 LEU cc_start: 0.9525 (mt) cc_final: 0.9315 (mt) REVERT: D 148 LEU cc_start: 0.8513 (mp) cc_final: 0.8017 (tp) REVERT: D 176 PHE cc_start: 0.7793 (m-10) cc_final: 0.7107 (m-80) REVERT: D 219 ASP cc_start: 0.8176 (t0) cc_final: 0.7952 (t0) REVERT: D 252 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8384 (ttp80) REVERT: D 260 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8857 (ttpp) REVERT: D 289 LEU cc_start: 0.7635 (tp) cc_final: 0.7377 (tp) REVERT: D 292 VAL cc_start: 0.7008 (p) cc_final: 0.6718 (p) REVERT: E 24 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8943 (mp10) REVERT: E 150 MET cc_start: 0.7554 (tpt) cc_final: 0.7308 (tpt) REVERT: E 173 PHE cc_start: 0.8699 (m-80) cc_final: 0.8489 (m-80) REVERT: E 291 ARG cc_start: 0.9498 (mtm110) cc_final: 0.9171 (mtm110) REVERT: E 295 HIS cc_start: 0.8871 (m-70) cc_final: 0.8607 (m90) REVERT: E 336 LEU cc_start: 0.9181 (mt) cc_final: 0.8896 (mt) REVERT: E 396 ILE cc_start: 0.9295 (pt) cc_final: 0.9030 (tp) REVERT: E 466 GLU cc_start: 0.8968 (pp20) cc_final: 0.8071 (pp20) REVERT: E 467 VAL cc_start: 0.9254 (t) cc_final: 0.9030 (t) REVERT: E 619 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8720 (tm-30) REVERT: E 634 LYS cc_start: 0.9471 (ptmt) cc_final: 0.8938 (mmtm) REVERT: F 129 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7073 (tp30) REVERT: F 176 PHE cc_start: 0.7850 (m-10) cc_final: 0.7499 (m-80) REVERT: F 206 LEU cc_start: 0.8418 (mm) cc_final: 0.7600 (mm) REVERT: F 219 ASP cc_start: 0.8197 (t70) cc_final: 0.7875 (t0) REVERT: F 233 CYS cc_start: 0.8107 (t) cc_final: 0.7491 (p) REVERT: F 259 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8442 (ttm170) REVERT: F 292 VAL cc_start: 0.7408 (t) cc_final: 0.7182 (t) REVERT: F 293 GLN cc_start: 0.6956 (tp40) cc_final: 0.6658 (tp-100) REVERT: G 287 ARG cc_start: 0.9077 (mmt180) cc_final: 0.8561 (mmp-170) REVERT: G 294 MET cc_start: 0.8796 (mmm) cc_final: 0.8400 (mmp) REVERT: G 303 GLU cc_start: 0.8950 (mp0) cc_final: 0.8647 (mp0) REVERT: G 396 ILE cc_start: 0.9196 (pt) cc_final: 0.8889 (tp) REVERT: G 466 GLU cc_start: 0.9124 (pp20) cc_final: 0.8221 (pp20) REVERT: G 467 VAL cc_start: 0.9309 (t) cc_final: 0.8954 (t) REVERT: G 470 CYS cc_start: 0.8386 (m) cc_final: 0.7860 (m) REVERT: G 473 ARG cc_start: 0.8535 (ptm160) cc_final: 0.8155 (mtm-85) REVERT: G 626 LYS cc_start: 0.9265 (ttpp) cc_final: 0.8921 (ttpp) REVERT: H 148 LEU cc_start: 0.8429 (mp) cc_final: 0.8189 (mp) REVERT: H 176 PHE cc_start: 0.7814 (m-10) cc_final: 0.7541 (m-80) REVERT: H 219 ASP cc_start: 0.8390 (t0) cc_final: 0.8172 (t0) REVERT: H 259 ARG cc_start: 0.8720 (ptp-170) cc_final: 0.8422 (ttp80) REVERT: H 289 LEU cc_start: 0.7613 (tp) cc_final: 0.7385 (tp) REVERT: H 399 GLU cc_start: 0.8636 (mp0) cc_final: 0.8030 (tm-30) REVERT: H 422 ASN cc_start: 0.7283 (t0) cc_final: 0.7028 (t0) REVERT: I 228 ASP cc_start: 0.8877 (p0) cc_final: 0.8599 (p0) REVERT: I 294 MET cc_start: 0.9195 (mmt) cc_final: 0.8950 (mmm) REVERT: I 336 LEU cc_start: 0.9350 (mt) cc_final: 0.9058 (mt) REVERT: I 466 GLU cc_start: 0.9081 (pp20) cc_final: 0.8492 (pp20) REVERT: I 473 ARG cc_start: 0.8746 (ptp-110) cc_final: 0.8438 (mtm-85) REVERT: I 618 CYS cc_start: 0.9055 (t) cc_final: 0.8660 (t) REVERT: I 619 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8917 (tm-30) REVERT: J 148 LEU cc_start: 0.8602 (mt) cc_final: 0.8294 (tp) REVERT: J 155 ASP cc_start: 0.9202 (t0) cc_final: 0.8742 (t70) REVERT: J 159 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8676 (mt-10) REVERT: J 219 ASP cc_start: 0.8046 (t70) cc_final: 0.7693 (t0) REVERT: J 289 LEU cc_start: 0.7902 (tp) cc_final: 0.7664 (tp) REVERT: J 305 VAL cc_start: 0.8528 (t) cc_final: 0.8325 (t) REVERT: K 139 VAL cc_start: 0.9696 (m) cc_final: 0.9383 (p) REVERT: K 291 ARG cc_start: 0.9463 (mtp-110) cc_final: 0.9170 (mtm110) REVERT: K 294 MET cc_start: 0.8863 (mmp) cc_final: 0.8594 (mmm) REVERT: K 295 HIS cc_start: 0.8755 (m-70) cc_final: 0.8540 (m90) REVERT: K 336 LEU cc_start: 0.9073 (mt) cc_final: 0.8859 (mt) REVERT: K 339 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8753 (tttp) REVERT: K 396 ILE cc_start: 0.9304 (pt) cc_final: 0.9060 (tp) REVERT: K 466 GLU cc_start: 0.9061 (pp20) cc_final: 0.8121 (pp20) REVERT: K 467 VAL cc_start: 0.9267 (t) cc_final: 0.9049 (t) REVERT: K 680 MET cc_start: 0.8287 (tmm) cc_final: 0.7766 (tmm) REVERT: K 710 TRP cc_start: 0.3827 (t-100) cc_final: 0.3339 (t-100) REVERT: L 129 GLU cc_start: 0.7667 (mt-10) cc_final: 0.6963 (tp30) REVERT: L 148 LEU cc_start: 0.8166 (mp) cc_final: 0.7704 (tp) REVERT: L 159 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8523 (mt-10) REVERT: L 176 PHE cc_start: 0.7041 (m-10) cc_final: 0.6765 (m-10) REVERT: L 219 ASP cc_start: 0.8454 (t70) cc_final: 0.8131 (t0) REVERT: L 289 LEU cc_start: 0.7567 (tp) cc_final: 0.7299 (tp) REVERT: L 422 ASN cc_start: 0.6662 (t0) cc_final: 0.6401 (t0) REVERT: M 24 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8799 (mp10) REVERT: M 139 VAL cc_start: 0.9571 (m) cc_final: 0.9352 (p) REVERT: M 220 MET cc_start: 0.5975 (tmm) cc_final: 0.5771 (ppp) REVERT: M 287 ARG cc_start: 0.9084 (mmt180) cc_final: 0.8668 (mmm160) REVERT: M 294 MET cc_start: 0.9193 (mmp) cc_final: 0.8758 (mmm) REVERT: M 379 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8398 (tm-30) REVERT: M 425 GLU cc_start: 0.8336 (pp20) cc_final: 0.8052 (pp20) REVERT: M 457 PHE cc_start: 0.9038 (m-80) cc_final: 0.8762 (m-80) REVERT: M 466 GLU cc_start: 0.8981 (pp20) cc_final: 0.8696 (pp20) REVERT: M 478 VAL cc_start: 0.9198 (t) cc_final: 0.8976 (t) REVERT: M 619 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8907 (tm-30) REVERT: M 638 ASP cc_start: 0.8007 (p0) cc_final: 0.7742 (p0) REVERT: M 642 LYS cc_start: 0.9423 (mttt) cc_final: 0.8695 (tttt) REVERT: N 168 PHE cc_start: 0.8774 (m-80) cc_final: 0.8517 (m-80) REVERT: N 192 ASP cc_start: 0.7582 (m-30) cc_final: 0.7350 (m-30) REVERT: N 219 ASP cc_start: 0.8673 (t70) cc_final: 0.8406 (t0) REVERT: N 260 LYS cc_start: 0.9404 (ttpp) cc_final: 0.9170 (ttpp) REVERT: N 268 TRP cc_start: 0.8693 (m100) cc_final: 0.8403 (m100) REVERT: N 289 LEU cc_start: 0.7685 (tp) cc_final: 0.7354 (tp) REVERT: O 110 GLU cc_start: 0.7610 (tt0) cc_final: 0.7165 (tt0) REVERT: O 122 ASN cc_start: 0.8792 (t0) cc_final: 0.8477 (t0) REVERT: O 133 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8848 (mmtt) REVERT: O 294 MET cc_start: 0.9036 (mmp) cc_final: 0.8583 (mmm) REVERT: O 300 CYS cc_start: 0.9066 (m) cc_final: 0.8763 (m) REVERT: O 336 LEU cc_start: 0.9232 (mt) cc_final: 0.9018 (mt) REVERT: O 426 GLU cc_start: 0.8380 (mp0) cc_final: 0.8111 (mp0) REVERT: O 456 ARG cc_start: 0.8462 (ttm110) cc_final: 0.7657 (ttm170) REVERT: O 464 ILE cc_start: 0.9444 (mt) cc_final: 0.9184 (mt) REVERT: O 466 GLU cc_start: 0.8949 (pp20) cc_final: 0.8267 (pp20) REVERT: O 467 VAL cc_start: 0.9184 (m) cc_final: 0.8712 (m) REVERT: O 618 CYS cc_start: 0.8807 (t) cc_final: 0.8432 (t) REVERT: O 619 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8832 (tm-30) REVERT: O 634 LYS cc_start: 0.9473 (ptmt) cc_final: 0.9125 (mmtm) REVERT: O 638 ASP cc_start: 0.8311 (p0) cc_final: 0.7997 (p0) REVERT: O 642 LYS cc_start: 0.9428 (mttt) cc_final: 0.8597 (tttp) REVERT: P 163 TYR cc_start: 0.8410 (m-10) cc_final: 0.7853 (m-10) REVERT: P 176 PHE cc_start: 0.7475 (m-10) cc_final: 0.6995 (m-10) REVERT: P 289 LEU cc_start: 0.7661 (tp) cc_final: 0.7405 (tp) outliers start: 0 outliers final: 0 residues processed: 2743 average time/residue: 1.3704 time to fit residues: 6108.2772 Evaluate side-chains 2526 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2526 time to evaluate : 6.495 ------------------------------------------------------------------------------- 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: 2.9990 chunk 633 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 413 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 10.0000 chunk 584 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 ASN ** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.7224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 58944 Z= 0.249 Angle : 0.578 7.516 80072 Z= 0.317 Chirality : 0.039 0.355 9440 Planarity : 0.005 0.065 10304 Dihedral : 6.096 57.152 8248 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.08 (0.10), residues: 7288 helix: 0.65 (0.08), residues: 4072 sheet: -1.47 (0.20), residues: 576 loop : -0.68 (0.13), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 268 HIS 0.006 0.001 HIS I 445 PHE 0.021 0.001 PHE M 374 TYR 0.018 0.002 TYR A 493 ARG 0.009 0.001 ARG G 403 *********************** 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 2759 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2759 time to evaluate : 6.511 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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8316 (tt0) cc_final: 0.7949 (tt0) REVERT: A 173 PHE cc_start: 0.8749 (m-80) cc_final: 0.8533 (m-80) REVERT: A 294 MET cc_start: 0.9013 (mmm) cc_final: 0.8566 (mmm) REVERT: A 336 LEU cc_start: 0.9252 (mt) cc_final: 0.8964 (mt) REVERT: A 444 GLN cc_start: 0.9104 (tp40) cc_final: 0.8745 (tm-30) REVERT: A 453 GLU cc_start: 0.8486 (mp0) cc_final: 0.8085 (mp0) REVERT: A 466 GLU cc_start: 0.8928 (pp20) cc_final: 0.8099 (pp20) REVERT: A 470 CYS cc_start: 0.8143 (m) cc_final: 0.7869 (m) REVERT: A 618 CYS cc_start: 0.8951 (t) cc_final: 0.8602 (t) REVERT: A 619 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8695 (tm-30) REVERT: A 672 ASP cc_start: 0.8160 (m-30) cc_final: 0.7732 (m-30) REVERT: B 155 ASP cc_start: 0.8952 (m-30) cc_final: 0.8698 (m-30) REVERT: B 176 PHE cc_start: 0.7713 (m-10) cc_final: 0.7210 (m-80) REVERT: B 219 ASP cc_start: 0.8150 (t0) cc_final: 0.7831 (t0) REVERT: B 277 CYS cc_start: 0.8495 (p) cc_final: 0.7617 (p) REVERT: B 289 LEU cc_start: 0.7284 (tp) cc_final: 0.7023 (tp) REVERT: B 293 GLN cc_start: 0.7025 (tt0) cc_final: 0.6109 (tp-100) REVERT: B 297 LEU cc_start: 0.8264 (tt) cc_final: 0.7759 (tt) REVERT: C 131 HIS cc_start: 0.8357 (t70) cc_final: 0.8141 (t70) REVERT: C 173 PHE cc_start: 0.8958 (m-80) cc_final: 0.8664 (m-80) REVERT: C 268 PHE cc_start: 0.9241 (t80) cc_final: 0.9032 (t80) REVERT: C 396 ILE cc_start: 0.9374 (pt) cc_final: 0.9150 (tp) REVERT: C 410 GLU cc_start: 0.8925 (pm20) cc_final: 0.8597 (pm20) REVERT: C 426 GLU cc_start: 0.8443 (mp0) cc_final: 0.8063 (mp0) REVERT: C 444 GLN cc_start: 0.9312 (tp40) cc_final: 0.8802 (tm-30) REVERT: C 619 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8874 (tm-30) REVERT: C 630 LEU cc_start: 0.9556 (mt) cc_final: 0.9314 (mt) REVERT: D 148 LEU cc_start: 0.8596 (mp) cc_final: 0.8061 (tp) REVERT: D 176 PHE cc_start: 0.7924 (m-10) cc_final: 0.7418 (m-80) REVERT: D 289 LEU cc_start: 0.7647 (tp) cc_final: 0.7380 (tp) REVERT: D 292 VAL cc_start: 0.6975 (p) cc_final: 0.6744 (p) REVERT: D 333 ASP cc_start: 0.8792 (t0) cc_final: 0.8589 (t0) REVERT: E 24 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8872 (mp10) REVERT: E 150 MET cc_start: 0.7622 (tpt) cc_final: 0.7408 (tpt) REVERT: E 287 ARG cc_start: 0.8899 (mmt180) cc_final: 0.8548 (mmm160) REVERT: E 291 ARG cc_start: 0.9450 (mtm110) cc_final: 0.9154 (mtm110) REVERT: E 294 MET cc_start: 0.8793 (mmp) cc_final: 0.8244 (mmm) REVERT: E 295 HIS cc_start: 0.8872 (m-70) cc_final: 0.8599 (m90) REVERT: E 336 LEU cc_start: 0.9284 (mt) cc_final: 0.9021 (mt) REVERT: E 396 ILE cc_start: 0.9282 (pt) cc_final: 0.9043 (tp) REVERT: E 426 GLU cc_start: 0.8521 (mp0) cc_final: 0.8268 (mp0) REVERT: E 466 GLU cc_start: 0.8943 (pp20) cc_final: 0.8041 (pp20) REVERT: E 467 VAL cc_start: 0.9267 (t) cc_final: 0.9059 (t) REVERT: E 619 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8709 (tm-30) REVERT: E 634 LYS cc_start: 0.9484 (ptmt) cc_final: 0.8973 (mmtm) REVERT: F 129 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7078 (tp30) REVERT: F 148 LEU cc_start: 0.8778 (tt) cc_final: 0.8557 (tp) REVERT: F 159 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8678 (mt-10) REVERT: F 176 PHE cc_start: 0.7857 (m-10) cc_final: 0.7496 (m-80) REVERT: F 206 LEU cc_start: 0.8467 (mm) cc_final: 0.7691 (mm) REVERT: F 219 ASP cc_start: 0.8178 (t70) cc_final: 0.7882 (t0) REVERT: F 233 CYS cc_start: 0.8136 (t) cc_final: 0.7515 (p) REVERT: F 292 VAL cc_start: 0.7636 (t) cc_final: 0.7386 (t) REVERT: F 293 GLN cc_start: 0.6995 (tp40) cc_final: 0.6721 (tp-100) REVERT: G 287 ARG cc_start: 0.9080 (mmt180) cc_final: 0.8532 (mmm160) REVERT: G 294 MET cc_start: 0.8954 (mmm) cc_final: 0.8683 (mmm) REVERT: G 303 GLU cc_start: 0.8929 (mp0) cc_final: 0.8605 (mp0) REVERT: G 396 ILE cc_start: 0.9235 (pt) cc_final: 0.8925 (tp) REVERT: G 426 GLU cc_start: 0.9070 (mp0) cc_final: 0.8835 (mp0) REVERT: G 466 GLU cc_start: 0.9103 (pp20) cc_final: 0.8168 (pp20) REVERT: G 467 VAL cc_start: 0.9328 (t) cc_final: 0.8985 (t) REVERT: G 470 CYS cc_start: 0.8312 (m) cc_final: 0.7849 (m) REVERT: G 473 ARG cc_start: 0.8538 (ptm160) cc_final: 0.8166 (mtm-85) REVERT: G 619 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8639 (tm-30) REVERT: G 634 LYS cc_start: 0.9478 (pttp) cc_final: 0.8959 (mmtm) REVERT: H 129 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7122 (tp30) REVERT: H 176 PHE cc_start: 0.7797 (m-10) cc_final: 0.7367 (m-80) REVERT: H 219 ASP cc_start: 0.8487 (t0) cc_final: 0.8285 (t0) REVERT: H 259 ARG cc_start: 0.8761 (ptp-170) cc_final: 0.8442 (ttp80) REVERT: H 289 LEU cc_start: 0.7600 (tp) cc_final: 0.7372 (tp) REVERT: H 422 ASN cc_start: 0.7268 (t0) cc_final: 0.7002 (t0) REVERT: I 228 ASP cc_start: 0.8780 (p0) cc_final: 0.8546 (p0) REVERT: I 294 MET cc_start: 0.9222 (mmt) cc_final: 0.9002 (mmm) REVERT: I 336 LEU cc_start: 0.9335 (mt) cc_final: 0.9038 (mt) REVERT: I 466 GLU cc_start: 0.9068 (pp20) cc_final: 0.8439 (pp20) REVERT: I 473 ARG cc_start: 0.8719 (ptp-110) cc_final: 0.8348 (mtm-85) REVERT: I 501 PHE cc_start: 0.8351 (t80) cc_final: 0.8106 (t80) REVERT: I 618 CYS cc_start: 0.9110 (t) cc_final: 0.8704 (t) REVERT: I 619 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8894 (tm-30) REVERT: I 620 VAL cc_start: 0.9286 (t) cc_final: 0.8839 (t) REVERT: J 148 LEU cc_start: 0.8621 (mt) cc_final: 0.8395 (tp) REVERT: J 155 ASP cc_start: 0.9203 (t0) cc_final: 0.8802 (t70) REVERT: J 159 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8737 (mt-10) REVERT: J 219 ASP cc_start: 0.8015 (t70) cc_final: 0.7660 (t0) REVERT: J 289 LEU cc_start: 0.7867 (tp) cc_final: 0.7634 (tp) REVERT: K 139 VAL cc_start: 0.9686 (m) cc_final: 0.9393 (p) REVERT: K 150 MET cc_start: 0.7829 (tpp) cc_final: 0.7325 (tpp) REVERT: K 291 ARG cc_start: 0.9477 (mtp-110) cc_final: 0.9188 (mtm110) REVERT: K 294 MET cc_start: 0.8842 (mmp) cc_final: 0.8600 (mmm) REVERT: K 295 HIS cc_start: 0.8746 (m-70) cc_final: 0.8515 (m90) REVERT: K 396 ILE cc_start: 0.9301 (pt) cc_final: 0.9059 (tp) REVERT: K 466 GLU cc_start: 0.9040 (pp20) cc_final: 0.8072 (pp20) REVERT: K 467 VAL cc_start: 0.9229 (t) cc_final: 0.9007 (t) REVERT: L 129 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6888 (tp30) REVERT: L 148 LEU cc_start: 0.8250 (mp) cc_final: 0.7970 (tp) REVERT: L 152 LEU cc_start: 0.8718 (mt) cc_final: 0.8309 (mt) REVERT: L 159 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8515 (mt-10) REVERT: L 176 PHE cc_start: 0.7111 (m-10) cc_final: 0.6860 (m-10) REVERT: L 219 ASP cc_start: 0.8429 (t70) cc_final: 0.8221 (t0) REVERT: L 289 LEU cc_start: 0.7564 (tp) cc_final: 0.7280 (tp) REVERT: M 24 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8734 (mp10) REVERT: M 139 VAL cc_start: 0.9635 (m) cc_final: 0.9420 (p) REVERT: M 220 MET cc_start: 0.6391 (tmm) cc_final: 0.6112 (ppp) REVERT: M 287 ARG cc_start: 0.9117 (mmt180) cc_final: 0.8687 (mmm160) REVERT: M 294 MET cc_start: 0.9202 (mmp) cc_final: 0.8773 (mmm) REVERT: M 379 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8220 (tm-30) REVERT: M 425 GLU cc_start: 0.8348 (pp20) cc_final: 0.8014 (pp20) REVERT: M 457 PHE cc_start: 0.9090 (m-80) cc_final: 0.8746 (m-80) REVERT: M 466 GLU cc_start: 0.8958 (pp20) cc_final: 0.8670 (pp20) REVERT: M 467 VAL cc_start: 0.9207 (t) cc_final: 0.8994 (t) REVERT: M 478 VAL cc_start: 0.9181 (t) cc_final: 0.8958 (t) REVERT: M 619 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8953 (tm-30) REVERT: M 630 LEU cc_start: 0.9519 (mt) cc_final: 0.9306 (mt) REVERT: M 638 ASP cc_start: 0.7965 (p0) cc_final: 0.7687 (p0) REVERT: M 642 LYS cc_start: 0.9413 (mttt) cc_final: 0.8679 (tttt) REVERT: N 219 ASP cc_start: 0.8685 (t70) cc_final: 0.8425 (t0) REVERT: N 260 LYS cc_start: 0.9438 (ttpp) cc_final: 0.9195 (ttpp) REVERT: N 268 TRP cc_start: 0.8707 (m100) cc_final: 0.8428 (m100) REVERT: N 289 LEU cc_start: 0.7609 (tp) cc_final: 0.7296 (tp) REVERT: N 394 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7371 (tm-30) REVERT: O 110 GLU cc_start: 0.7805 (tt0) cc_final: 0.7434 (tt0) REVERT: O 122 ASN cc_start: 0.8789 (t0) cc_final: 0.8433 (t0) REVERT: O 294 MET cc_start: 0.9055 (mmp) cc_final: 0.8699 (mmm) REVERT: O 300 CYS cc_start: 0.9044 (m) cc_final: 0.8772 (m) REVERT: O 336 LEU cc_start: 0.9244 (mt) cc_final: 0.8869 (mt) REVERT: O 426 GLU cc_start: 0.8373 (mp0) cc_final: 0.8142 (mp0) REVERT: O 464 ILE cc_start: 0.9466 (mt) cc_final: 0.9194 (mt) REVERT: O 466 GLU cc_start: 0.8939 (pp20) cc_final: 0.7987 (pp20) REVERT: O 470 CYS cc_start: 0.8230 (m) cc_final: 0.7966 (m) REVERT: O 618 CYS cc_start: 0.8827 (t) cc_final: 0.8567 (t) REVERT: O 619 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8847 (tm-30) REVERT: O 634 LYS cc_start: 0.9462 (ptmt) cc_final: 0.9117 (mmtm) REVERT: O 638 ASP cc_start: 0.8265 (p0) cc_final: 0.7979 (p0) REVERT: O 642 LYS cc_start: 0.9432 (mttt) cc_final: 0.8551 (tttp) REVERT: P 163 TYR cc_start: 0.8487 (m-10) cc_final: 0.7816 (m-10) REVERT: P 176 PHE cc_start: 0.7491 (m-10) cc_final: 0.7026 (m-10) REVERT: P 289 LEU cc_start: 0.7839 (tp) cc_final: 0.7534 (tp) outliers start: 0 outliers final: 0 residues processed: 2759 average time/residue: 1.4546 time to fit residues: 6570.8540 Evaluate side-chains 2543 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2543 time to evaluate : 6.521 ------------------------------------------------------------------------------- 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: 9.9990 chunk 401 optimal weight: 5.9990 chunk 514 optimal weight: 8.9990 chunk 398 optimal weight: 0.2980 chunk 592 optimal weight: 0.9980 chunk 393 optimal weight: 3.9990 chunk 701 optimal weight: 0.9990 chunk 439 optimal weight: 0.6980 chunk 427 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN E 440 GLN G 420 GLN I 420 GLN ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 58944 Z= 0.156 Angle : 0.516 7.601 80072 Z= 0.274 Chirality : 0.039 0.359 9440 Planarity : 0.005 0.060 10304 Dihedral : 5.895 57.192 8248 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.97 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 0.51 (0.10), residues: 7288 helix: 1.18 (0.08), residues: 4104 sheet: -1.40 (0.21), residues: 576 loop : -0.48 (0.13), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 268 HIS 0.005 0.001 HIS F 193 PHE 0.031 0.001 PHE C 457 TYR 0.026 0.001 TYR K 322 ARG 0.010 0.000 ARG G 441 *********************** 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 2811 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2811 time to evaluate : 6.151 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: 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.9137 (t0) cc_final: 0.8924 (t0) REVERT: A 173 PHE cc_start: 0.8702 (m-80) cc_final: 0.8487 (m-80) REVERT: A 294 MET cc_start: 0.9016 (mmm) cc_final: 0.8799 (mmm) REVERT: A 336 LEU cc_start: 0.9223 (mt) cc_final: 0.8917 (mt) REVERT: A 398 ASN cc_start: 0.8944 (m-40) cc_final: 0.8634 (m110) REVERT: A 429 LEU cc_start: 0.9349 (mm) cc_final: 0.9064 (mm) REVERT: A 444 GLN cc_start: 0.9012 (tp40) cc_final: 0.8730 (tp40) REVERT: A 466 GLU cc_start: 0.8865 (pp20) cc_final: 0.7975 (pp20) REVERT: A 470 CYS cc_start: 0.8167 (m) cc_final: 0.7931 (m) REVERT: A 618 CYS cc_start: 0.8940 (t) cc_final: 0.8522 (t) REVERT: A 619 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8705 (tm-30) REVERT: A 620 VAL cc_start: 0.9270 (t) cc_final: 0.8699 (t) REVERT: A 671 ASP cc_start: 0.7536 (p0) cc_final: 0.7335 (p0) REVERT: B 159 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8792 (mt-10) REVERT: B 176 PHE cc_start: 0.7605 (m-10) cc_final: 0.6918 (m-80) REVERT: B 219 ASP cc_start: 0.8217 (t0) cc_final: 0.7897 (t0) REVERT: B 277 CYS cc_start: 0.8446 (p) cc_final: 0.7587 (p) REVERT: B 289 LEU cc_start: 0.7302 (tp) cc_final: 0.7071 (tp) REVERT: B 293 GLN cc_start: 0.7014 (tt0) cc_final: 0.6196 (tp-100) REVERT: B 297 LEU cc_start: 0.8259 (tt) cc_final: 0.7680 (tt) REVERT: C 89 GLU cc_start: 0.7445 (mp0) cc_final: 0.6795 (mp0) REVERT: C 110 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 131 HIS cc_start: 0.8307 (t70) cc_final: 0.8047 (t70) REVERT: C 173 PHE cc_start: 0.8914 (m-80) cc_final: 0.8565 (m-80) REVERT: C 176 ASN cc_start: 0.8713 (t0) cc_final: 0.8317 (t0) REVERT: C 178 ASN cc_start: 0.8275 (t0) cc_final: 0.7735 (t0) REVERT: C 278 ASN cc_start: 0.8045 (p0) cc_final: 0.7842 (p0) REVERT: C 379 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8239 (tm-30) REVERT: C 396 ILE cc_start: 0.9350 (pt) cc_final: 0.9136 (tp) REVERT: C 426 GLU cc_start: 0.8349 (mp0) cc_final: 0.7924 (mp0) REVERT: C 429 LEU cc_start: 0.9280 (mp) cc_final: 0.8799 (mm) REVERT: C 444 GLN cc_start: 0.9294 (tp40) cc_final: 0.8770 (tm-30) REVERT: C 448 ASN cc_start: 0.9029 (m-40) cc_final: 0.8613 (m110) REVERT: C 466 GLU cc_start: 0.8884 (pp20) cc_final: 0.8271 (pp20) REVERT: C 478 VAL cc_start: 0.9047 (t) cc_final: 0.8826 (t) REVERT: C 485 ASN cc_start: 0.8868 (m110) cc_final: 0.8631 (m110) REVERT: C 619 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8834 (tm-30) REVERT: C 630 LEU cc_start: 0.9488 (mt) cc_final: 0.9253 (mt) REVERT: D 148 LEU cc_start: 0.8584 (mp) cc_final: 0.8136 (tp) REVERT: D 176 PHE cc_start: 0.7846 (m-10) cc_final: 0.7338 (m-80) REVERT: D 219 ASP cc_start: 0.8416 (t70) cc_final: 0.8077 (t0) REVERT: D 283 MET cc_start: 0.7880 (ppp) cc_final: 0.7483 (ppp) REVERT: D 289 LEU cc_start: 0.7695 (tp) cc_final: 0.7435 (tp) REVERT: D 292 VAL cc_start: 0.6915 (p) cc_final: 0.6499 (p) REVERT: D 333 ASP cc_start: 0.8736 (t0) cc_final: 0.8534 (t0) REVERT: E 24 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8803 (mp10) REVERT: E 150 MET cc_start: 0.7531 (tpt) cc_final: 0.7323 (tpt) REVERT: E 220 MET cc_start: 0.5805 (ppp) cc_final: 0.5593 (ppp) REVERT: E 291 ARG cc_start: 0.9437 (mtm110) cc_final: 0.9158 (mtm110) REVERT: E 294 MET cc_start: 0.8573 (mmp) cc_final: 0.8227 (mmm) REVERT: E 295 HIS cc_start: 0.8891 (m-70) cc_final: 0.8567 (m90) REVERT: E 336 LEU cc_start: 0.9196 (mt) cc_final: 0.8937 (mt) REVERT: E 396 ILE cc_start: 0.9272 (pt) cc_final: 0.9045 (tp) REVERT: E 426 GLU cc_start: 0.8518 (mp0) cc_final: 0.8201 (mp0) REVERT: E 466 GLU cc_start: 0.8879 (pp20) cc_final: 0.7940 (pp20) REVERT: E 619 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8684 (tm-30) REVERT: E 622 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8798 (mt-10) REVERT: E 633 ARG cc_start: 0.9075 (ptt180) cc_final: 0.8551 (ptt90) REVERT: E 634 LYS cc_start: 0.9462 (ptmt) cc_final: 0.8901 (mmtm) REVERT: F 129 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7060 (tp30) REVERT: F 148 LEU cc_start: 0.8776 (tt) cc_final: 0.8552 (tp) REVERT: F 159 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8695 (mt-10) REVERT: F 176 PHE cc_start: 0.7826 (m-10) cc_final: 0.7450 (m-80) REVERT: F 206 LEU cc_start: 0.8511 (mm) cc_final: 0.7672 (mm) REVERT: F 219 ASP cc_start: 0.8093 (t70) cc_final: 0.7797 (t0) REVERT: F 233 CYS cc_start: 0.8134 (t) cc_final: 0.7457 (p) REVERT: F 292 VAL cc_start: 0.7318 (t) cc_final: 0.7078 (t) REVERT: F 293 GLN cc_start: 0.7002 (tp40) cc_final: 0.6687 (tp-100) REVERT: G 258 VAL cc_start: 0.9259 (m) cc_final: 0.9023 (m) REVERT: G 263 ARG cc_start: 0.8667 (mmp80) cc_final: 0.8464 (mmp80) REVERT: G 287 ARG cc_start: 0.9059 (mmt180) cc_final: 0.8499 (mmm160) REVERT: G 294 MET cc_start: 0.8992 (mmm) cc_final: 0.8719 (mmm) REVERT: G 303 GLU cc_start: 0.8994 (mp0) cc_final: 0.8702 (mp0) REVERT: G 336 LEU cc_start: 0.9234 (mt) cc_final: 0.8938 (mt) REVERT: G 396 ILE cc_start: 0.9156 (pt) cc_final: 0.8872 (tp) REVERT: G 456 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7914 (ttm110) REVERT: G 466 GLU cc_start: 0.9080 (pp20) cc_final: 0.8108 (pp20) REVERT: G 467 VAL cc_start: 0.9272 (t) cc_final: 0.8933 (t) REVERT: G 470 CYS cc_start: 0.8325 (m) cc_final: 0.7885 (m) REVERT: G 473 ARG cc_start: 0.8417 (ptm160) cc_final: 0.8059 (mtm-85) REVERT: G 619 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8630 (tm-30) REVERT: G 633 ARG cc_start: 0.9132 (ptt180) cc_final: 0.8639 (ptt90) REVERT: G 634 LYS cc_start: 0.9441 (pttp) cc_final: 0.8829 (mmtm) REVERT: G 649 VAL cc_start: 0.9190 (t) cc_final: 0.8963 (t) REVERT: H 176 PHE cc_start: 0.7869 (m-10) cc_final: 0.7622 (m-80) REVERT: H 219 ASP cc_start: 0.8512 (t0) cc_final: 0.8294 (t0) REVERT: H 259 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8443 (ttp80) REVERT: H 289 LEU cc_start: 0.7510 (tp) cc_final: 0.7286 (tp) REVERT: H 399 GLU cc_start: 0.8608 (mp0) cc_final: 0.8018 (tm-30) REVERT: H 422 ASN cc_start: 0.7265 (t0) cc_final: 0.6994 (t0) REVERT: I 15 PHE cc_start: 0.8839 (m-80) cc_final: 0.8478 (m-80) REVERT: I 195 GLU cc_start: 0.8972 (tp30) cc_final: 0.8625 (tp30) REVERT: I 287 ARG cc_start: 0.8930 (mmt180) cc_final: 0.8719 (mmt180) REVERT: I 336 LEU cc_start: 0.9279 (mt) cc_final: 0.9014 (mt) REVERT: I 466 GLU cc_start: 0.9012 (pp20) cc_final: 0.8391 (pp20) REVERT: I 473 ARG cc_start: 0.8661 (ptp-110) cc_final: 0.8356 (mtm-85) REVERT: I 476 LEU cc_start: 0.9047 (tp) cc_final: 0.8845 (tp) REVERT: I 501 PHE cc_start: 0.8311 (t80) cc_final: 0.8088 (t80) REVERT: I 618 CYS cc_start: 0.9013 (t) cc_final: 0.8613 (t) REVERT: I 619 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8927 (tm-30) REVERT: I 620 VAL cc_start: 0.9192 (t) cc_final: 0.8738 (t) REVERT: J 148 LEU cc_start: 0.8698 (mt) cc_final: 0.8395 (tp) REVERT: J 155 ASP cc_start: 0.9202 (t0) cc_final: 0.8861 (t70) REVERT: J 159 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8711 (mt-10) REVERT: J 176 PHE cc_start: 0.7747 (m-10) cc_final: 0.7501 (m-10) REVERT: J 219 ASP cc_start: 0.7995 (t70) cc_final: 0.7656 (t0) REVERT: J 289 LEU cc_start: 0.7876 (tp) cc_final: 0.7641 (tp) REVERT: K 139 VAL cc_start: 0.9668 (m) cc_final: 0.9377 (p) REVERT: K 150 MET cc_start: 0.7673 (tpp) cc_final: 0.7208 (tpp) REVERT: K 291 ARG cc_start: 0.9437 (mtp-110) cc_final: 0.9213 (mtm110) REVERT: K 322 TYR cc_start: 0.7993 (p90) cc_final: 0.7784 (p90) REVERT: K 336 LEU cc_start: 0.9172 (mt) cc_final: 0.8909 (mt) REVERT: K 396 ILE cc_start: 0.9318 (pt) cc_final: 0.9092 (tp) REVERT: K 420 GLN cc_start: 0.8541 (mm110) cc_final: 0.8337 (mm110) REVERT: K 439 MET cc_start: 0.8591 (mmm) cc_final: 0.8114 (mmm) REVERT: K 466 GLU cc_start: 0.8948 (pp20) cc_final: 0.8003 (pp20) REVERT: K 467 VAL cc_start: 0.9149 (t) cc_final: 0.8936 (t) REVERT: K 703 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8369 (mt-10) REVERT: L 129 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6877 (tp30) REVERT: L 148 LEU cc_start: 0.8236 (mp) cc_final: 0.7826 (tp) REVERT: L 159 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8479 (mt-10) REVERT: L 289 LEU cc_start: 0.7506 (tp) cc_final: 0.7246 (tp) REVERT: L 292 VAL cc_start: 0.7156 (p) cc_final: 0.6912 (p) REVERT: L 422 ASN cc_start: 0.6693 (t0) cc_final: 0.6459 (t0) REVERT: M 24 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8703 (mp10) REVERT: M 220 MET cc_start: 0.6379 (tmm) cc_final: 0.5911 (ppp) REVERT: M 287 ARG cc_start: 0.9107 (mmt180) cc_final: 0.8692 (mmm160) REVERT: M 294 MET cc_start: 0.9104 (mmp) cc_final: 0.8695 (mmp) REVERT: M 336 LEU cc_start: 0.9226 (mt) cc_final: 0.9008 (mt) REVERT: M 379 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8197 (tm-30) REVERT: M 425 GLU cc_start: 0.8242 (pp20) cc_final: 0.7937 (pp20) REVERT: M 457 PHE cc_start: 0.8935 (m-80) cc_final: 0.8607 (m-80) REVERT: M 466 GLU cc_start: 0.8892 (pp20) cc_final: 0.8545 (pp20) REVERT: M 467 VAL cc_start: 0.9147 (t) cc_final: 0.8931 (t) REVERT: M 619 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8954 (tm-30) REVERT: M 620 VAL cc_start: 0.9315 (t) cc_final: 0.8836 (t) REVERT: M 630 LEU cc_start: 0.9479 (mt) cc_final: 0.9239 (mt) REVERT: M 638 ASP cc_start: 0.7771 (p0) cc_final: 0.7480 (p0) REVERT: M 642 LYS cc_start: 0.9240 (mttt) cc_final: 0.8453 (tttt) REVERT: M 672 ASP cc_start: 0.8020 (m-30) cc_final: 0.7437 (m-30) REVERT: N 192 ASP cc_start: 0.7951 (m-30) cc_final: 0.6732 (m-30) REVERT: N 260 LYS cc_start: 0.9436 (ttpp) cc_final: 0.9197 (ttpp) REVERT: N 289 LEU cc_start: 0.7672 (tp) cc_final: 0.7341 (tp) REVERT: O 89 GLU cc_start: 0.7962 (pm20) cc_final: 0.7204 (pm20) REVERT: O 122 ASN cc_start: 0.8700 (t0) cc_final: 0.8334 (t0) REVERT: O 294 MET cc_start: 0.9004 (mmp) cc_final: 0.8703 (mmm) REVERT: O 336 LEU cc_start: 0.9212 (mt) cc_final: 0.8832 (mt) REVERT: O 394 THR cc_start: 0.9214 (p) cc_final: 0.8985 (p) REVERT: O 398 ASN cc_start: 0.8768 (m110) cc_final: 0.8548 (m110) REVERT: O 423 ARG cc_start: 0.8719 (mtt180) cc_final: 0.8457 (ttm110) REVERT: O 426 GLU cc_start: 0.8308 (mp0) cc_final: 0.8102 (mp0) REVERT: O 456 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7978 (ttm-80) REVERT: O 464 ILE cc_start: 0.9426 (mt) cc_final: 0.9213 (mt) REVERT: O 466 GLU cc_start: 0.8921 (pp20) cc_final: 0.7992 (pp20) REVERT: O 470 CYS cc_start: 0.8180 (m) cc_final: 0.7866 (m) REVERT: O 618 CYS cc_start: 0.8766 (t) cc_final: 0.8429 (t) REVERT: O 619 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8805 (tm-30) REVERT: O 638 ASP cc_start: 0.8109 (p0) cc_final: 0.7857 (p0) REVERT: O 642 LYS cc_start: 0.9275 (mttt) cc_final: 0.8320 (tttt) REVERT: P 163 TYR cc_start: 0.8483 (m-10) cc_final: 0.7756 (m-10) REVERT: P 176 PHE cc_start: 0.7472 (m-10) cc_final: 0.7002 (m-10) REVERT: P 289 LEU cc_start: 0.7929 (tp) cc_final: 0.7630 (tp) REVERT: P 333 ASP cc_start: 0.8762 (t0) cc_final: 0.8556 (t0) outliers start: 0 outliers final: 0 residues processed: 2811 average time/residue: 1.3878 time to fit residues: 6340.1662 Evaluate side-chains 2570 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2570 time to evaluate : 6.446 ------------------------------------------------------------------------------- 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: 10.0000 chunk 280 optimal weight: 7.9990 chunk 419 optimal weight: 2.9990 chunk 211 optimal weight: 0.0980 chunk 137 optimal weight: 0.5980 chunk 135 optimal weight: 0.0000 chunk 446 optimal weight: 6.9990 chunk 478 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 551 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 635 ASN I 27 GLN I 34 GLN I 335 GLN ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 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** O 448 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 58944 Z= 0.165 Angle : 0.517 7.378 80072 Z= 0.278 Chirality : 0.039 0.350 9440 Planarity : 0.005 0.072 10304 Dihedral : 5.775 55.633 8248 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.69 (0.10), residues: 7288 helix: 1.33 (0.08), residues: 4096 sheet: -1.35 (0.21), residues: 576 loop : -0.42 (0.13), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 268 HIS 0.012 0.001 HIS B 348 PHE 0.027 0.001 PHE I 93 TYR 0.029 0.001 TYR L 444 ARG 0.011 0.000 ARG C 279 *********************** 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 2761 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2761 time to evaluate : 6.658 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 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.9137 (t0) cc_final: 0.8923 (t0) REVERT: A 173 PHE cc_start: 0.8714 (m-80) cc_final: 0.8495 (m-80) REVERT: A 336 LEU cc_start: 0.9198 (mt) cc_final: 0.8831 (mt) REVERT: A 429 LEU cc_start: 0.9388 (mm) cc_final: 0.9152 (mm) REVERT: A 444 GLN cc_start: 0.9033 (tp40) cc_final: 0.8590 (tm-30) REVERT: A 453 GLU cc_start: 0.8635 (mp0) cc_final: 0.8248 (mp0) REVERT: A 466 GLU cc_start: 0.8856 (pp20) cc_final: 0.7980 (pp20) REVERT: A 470 CYS cc_start: 0.8059 (m) cc_final: 0.7847 (m) REVERT: A 618 CYS cc_start: 0.8926 (t) cc_final: 0.8555 (t) REVERT: A 619 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8686 (tm-30) REVERT: A 620 VAL cc_start: 0.9266 (t) cc_final: 0.8691 (t) REVERT: B 159 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8881 (mt-10) REVERT: B 176 PHE cc_start: 0.7536 (m-10) cc_final: 0.6741 (m-80) REVERT: B 219 ASP cc_start: 0.8206 (t0) cc_final: 0.7885 (t0) REVERT: B 275 LEU cc_start: 0.7401 (mt) cc_final: 0.6856 (mp) REVERT: B 277 CYS cc_start: 0.8489 (p) cc_final: 0.7614 (p) REVERT: B 289 LEU cc_start: 0.7373 (tp) cc_final: 0.7145 (tp) REVERT: B 292 VAL cc_start: 0.7275 (p) cc_final: 0.6977 (p) REVERT: B 293 GLN cc_start: 0.7058 (tt0) cc_final: 0.6151 (tp-100) REVERT: B 297 LEU cc_start: 0.8305 (tt) cc_final: 0.7715 (tt) REVERT: C 131 HIS cc_start: 0.8330 (t70) cc_final: 0.8023 (t70) REVERT: C 173 PHE cc_start: 0.8923 (m-80) cc_final: 0.8593 (m-80) REVERT: C 379 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 396 ILE cc_start: 0.9361 (pt) cc_final: 0.9139 (tp) REVERT: C 426 GLU cc_start: 0.8416 (mp0) cc_final: 0.8081 (mp0) REVERT: C 444 GLN cc_start: 0.9310 (tp40) cc_final: 0.8800 (tm-30) REVERT: C 466 GLU cc_start: 0.8901 (pp20) cc_final: 0.8304 (pp20) REVERT: C 619 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8835 (tm-30) REVERT: C 620 VAL cc_start: 0.9304 (t) cc_final: 0.8715 (t) REVERT: C 630 LEU cc_start: 0.9479 (mt) cc_final: 0.9254 (mt) REVERT: D 148 LEU cc_start: 0.8539 (mp) cc_final: 0.8144 (tp) REVERT: D 176 PHE cc_start: 0.7862 (m-10) cc_final: 0.7398 (m-80) REVERT: D 219 ASP cc_start: 0.8432 (t70) cc_final: 0.8099 (t0) REVERT: D 283 MET cc_start: 0.7949 (ppp) cc_final: 0.7641 (ppp) REVERT: D 289 LEU cc_start: 0.7675 (tp) cc_final: 0.7429 (tp) REVERT: E 24 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8826 (mp10) REVERT: E 28 ILE cc_start: 0.8620 (mp) cc_final: 0.8045 (mm) REVERT: E 150 MET cc_start: 0.7506 (tpt) cc_final: 0.7294 (tpt) REVERT: E 291 ARG cc_start: 0.9444 (mtm110) cc_final: 0.9141 (mtm110) REVERT: E 294 MET cc_start: 0.8601 (mmp) cc_final: 0.8290 (mmm) REVERT: E 295 HIS cc_start: 0.8850 (m-70) cc_final: 0.8597 (m90) REVERT: E 336 LEU cc_start: 0.9186 (mt) cc_final: 0.8939 (mt) REVERT: E 396 ILE cc_start: 0.9281 (pt) cc_final: 0.9070 (tp) REVERT: E 426 GLU cc_start: 0.8520 (mp0) cc_final: 0.8261 (mp0) REVERT: E 466 GLU cc_start: 0.8874 (pp20) cc_final: 0.7930 (pp20) REVERT: E 619 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8688 (tm-30) REVERT: E 622 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8799 (mt-10) REVERT: E 633 ARG cc_start: 0.9080 (ptt180) cc_final: 0.8578 (ptt90) REVERT: E 634 LYS cc_start: 0.9488 (ptmt) cc_final: 0.8949 (mmtm) REVERT: F 129 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7002 (tp30) REVERT: F 148 LEU cc_start: 0.8789 (tt) cc_final: 0.8394 (tp) REVERT: F 159 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8772 (mt-10) REVERT: F 176 PHE cc_start: 0.7818 (m-10) cc_final: 0.7474 (m-80) REVERT: F 206 LEU cc_start: 0.8538 (mm) cc_final: 0.7695 (mm) REVERT: F 219 ASP cc_start: 0.8152 (t70) cc_final: 0.7803 (t0) REVERT: F 233 CYS cc_start: 0.8160 (t) cc_final: 0.7459 (p) REVERT: F 292 VAL cc_start: 0.7244 (t) cc_final: 0.6943 (t) REVERT: F 293 GLN cc_start: 0.6769 (tp40) cc_final: 0.6466 (tp40) REVERT: G 294 MET cc_start: 0.9022 (mmm) cc_final: 0.8706 (mmm) REVERT: G 303 GLU cc_start: 0.8958 (mp0) cc_final: 0.8690 (mp0) REVERT: G 396 ILE cc_start: 0.9194 (pt) cc_final: 0.8908 (tp) REVERT: G 456 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7838 (ttm-80) REVERT: G 466 GLU cc_start: 0.9084 (pp20) cc_final: 0.8111 (pp20) REVERT: G 467 VAL cc_start: 0.9254 (t) cc_final: 0.8896 (t) REVERT: G 470 CYS cc_start: 0.8331 (m) cc_final: 0.7938 (m) REVERT: G 473 ARG cc_start: 0.8473 (ptm160) cc_final: 0.8095 (mtm-85) REVERT: G 489 ILE cc_start: 0.8784 (mm) cc_final: 0.8504 (mm) REVERT: G 619 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8664 (tm-30) REVERT: G 633 ARG cc_start: 0.9159 (ptt180) cc_final: 0.8654 (ptt90) REVERT: G 634 LYS cc_start: 0.9452 (pttp) cc_final: 0.8865 (mmtm) REVERT: G 635 ASN cc_start: 0.8923 (m-40) cc_final: 0.8706 (m-40) REVERT: G 649 VAL cc_start: 0.9201 (t) cc_final: 0.8935 (t) REVERT: G 680 MET cc_start: 0.8292 (tmm) cc_final: 0.7909 (tmm) REVERT: H 129 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7080 (tp30) REVERT: H 176 PHE cc_start: 0.7844 (m-10) cc_final: 0.7598 (m-80) REVERT: H 219 ASP cc_start: 0.8499 (t0) cc_final: 0.8275 (t0) REVERT: H 289 LEU cc_start: 0.7492 (tp) cc_final: 0.7274 (tp) REVERT: H 422 ASN cc_start: 0.7287 (t0) cc_final: 0.7022 (t0) REVERT: I 15 PHE cc_start: 0.8876 (m-80) cc_final: 0.8523 (m-80) REVERT: I 195 GLU cc_start: 0.9028 (tp30) cc_final: 0.8667 (tp30) REVERT: I 220 MET cc_start: 0.7255 (ttp) cc_final: 0.6322 (ppp) REVERT: I 287 ARG cc_start: 0.8945 (mmt180) cc_final: 0.8729 (mmt180) REVERT: I 294 MET cc_start: 0.9223 (mmp) cc_final: 0.8715 (mmm) REVERT: I 336 LEU cc_start: 0.9263 (mt) cc_final: 0.8918 (mt) REVERT: I 466 GLU cc_start: 0.9017 (pp20) cc_final: 0.8377 (pp20) REVERT: I 473 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.8282 (mtm-85) REVERT: I 501 PHE cc_start: 0.8346 (t80) cc_final: 0.8110 (t80) REVERT: I 618 CYS cc_start: 0.8934 (t) cc_final: 0.8572 (t) REVERT: I 619 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8927 (tm-30) REVERT: I 620 VAL cc_start: 0.9175 (t) cc_final: 0.8721 (t) REVERT: J 148 LEU cc_start: 0.8703 (mt) cc_final: 0.8399 (tp) REVERT: J 155 ASP cc_start: 0.9207 (t0) cc_final: 0.8893 (t70) REVERT: J 159 GLU cc_start: 0.9402 (mm-30) cc_final: 0.8844 (mt-10) REVERT: J 176 PHE cc_start: 0.7760 (m-10) cc_final: 0.7550 (m-80) REVERT: J 219 ASP cc_start: 0.8002 (t70) cc_final: 0.7652 (t0) REVERT: K 139 VAL cc_start: 0.9666 (m) cc_final: 0.9386 (p) REVERT: K 150 MET cc_start: 0.7570 (tpp) cc_final: 0.7154 (tpp) REVERT: K 291 ARG cc_start: 0.9469 (mtp-110) cc_final: 0.9208 (mtm110) REVERT: K 295 HIS cc_start: 0.8832 (m90) cc_final: 0.8548 (m90) REVERT: K 300 CYS cc_start: 0.9121 (m) cc_final: 0.8887 (m) REVERT: K 322 TYR cc_start: 0.7984 (p90) cc_final: 0.7747 (p90) REVERT: K 324 GLU cc_start: 0.7260 (mp0) cc_final: 0.7038 (mp0) REVERT: K 336 LEU cc_start: 0.9171 (mt) cc_final: 0.8886 (mt) REVERT: K 396 ILE cc_start: 0.9327 (pt) cc_final: 0.9094 (tp) REVERT: K 407 PHE cc_start: 0.6255 (p90) cc_final: 0.5935 (p90) REVERT: K 466 GLU cc_start: 0.8954 (pp20) cc_final: 0.8034 (pp20) REVERT: K 467 VAL cc_start: 0.9129 (t) cc_final: 0.8910 (t) REVERT: L 129 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6945 (tp30) REVERT: L 148 LEU cc_start: 0.8262 (mp) cc_final: 0.7888 (tp) REVERT: L 159 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8491 (mt-10) REVERT: L 289 LEU cc_start: 0.7498 (tp) cc_final: 0.7229 (tp) REVERT: L 292 VAL cc_start: 0.7198 (p) cc_final: 0.6965 (p) REVERT: L 422 ASN cc_start: 0.6713 (t0) cc_final: 0.6471 (t0) REVERT: M 15 PHE cc_start: 0.9013 (m-80) cc_final: 0.8724 (m-80) REVERT: M 24 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8712 (mp10) REVERT: M 89 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6917 (tm-30) REVERT: M 220 MET cc_start: 0.6571 (tmm) cc_final: 0.6113 (ppp) REVERT: M 287 ARG cc_start: 0.9104 (mmt180) cc_final: 0.8666 (mmm160) REVERT: M 294 MET cc_start: 0.9112 (mmp) cc_final: 0.8686 (mmp) REVERT: M 324 GLU cc_start: 0.7562 (pm20) cc_final: 0.7323 (mp0) REVERT: M 336 LEU cc_start: 0.9228 (mt) cc_final: 0.9004 (mt) REVERT: M 379 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8172 (tm-30) REVERT: M 425 GLU cc_start: 0.8209 (pp20) cc_final: 0.7939 (pp20) REVERT: M 466 GLU cc_start: 0.8889 (pp20) cc_final: 0.8538 (pp20) REVERT: M 467 VAL cc_start: 0.9145 (t) cc_final: 0.8925 (t) REVERT: M 619 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8952 (tm-30) REVERT: M 620 VAL cc_start: 0.9290 (t) cc_final: 0.8820 (t) REVERT: M 630 LEU cc_start: 0.9476 (mt) cc_final: 0.9249 (mt) REVERT: M 638 ASP cc_start: 0.7743 (p0) cc_final: 0.7462 (p0) REVERT: M 642 LYS cc_start: 0.9264 (mttt) cc_final: 0.8462 (tttt) REVERT: M 680 MET cc_start: 0.7754 (tmm) cc_final: 0.7096 (tmm) REVERT: N 256 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8451 (mt-10) REVERT: N 260 LYS cc_start: 0.9447 (ttpp) cc_final: 0.9232 (ttpp) REVERT: N 289 LEU cc_start: 0.7832 (tp) cc_final: 0.7517 (tp) REVERT: N 394 GLU cc_start: 0.8157 (mp0) cc_final: 0.7905 (mp0) REVERT: N 395 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8633 (mp0) REVERT: O 89 GLU cc_start: 0.7878 (pm20) cc_final: 0.7218 (pm20) REVERT: O 122 ASN cc_start: 0.8680 (t0) cc_final: 0.8321 (t0) REVERT: O 178 ASN cc_start: 0.8470 (t0) cc_final: 0.8242 (t0) REVERT: O 227 MET cc_start: 0.8952 (mmm) cc_final: 0.8733 (mmm) REVERT: O 278 ASN cc_start: 0.7106 (p0) cc_final: 0.6821 (p0) REVERT: O 294 MET cc_start: 0.9024 (mmp) cc_final: 0.8700 (mmm) REVERT: O 336 LEU cc_start: 0.9168 (mt) cc_final: 0.8754 (mt) REVERT: O 420 GLN cc_start: 0.8137 (mm110) cc_final: 0.7896 (mm-40) REVERT: O 423 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8517 (ttm110) REVERT: O 426 GLU cc_start: 0.8330 (mp0) cc_final: 0.8079 (mp0) REVERT: O 456 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8065 (ttm-80) REVERT: O 464 ILE cc_start: 0.9458 (mt) cc_final: 0.9238 (mt) REVERT: O 466 GLU cc_start: 0.8917 (pp20) cc_final: 0.8000 (pp20) REVERT: O 470 CYS cc_start: 0.8134 (m) cc_final: 0.7838 (m) REVERT: O 618 CYS cc_start: 0.8750 (t) cc_final: 0.8280 (t) REVERT: O 619 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8831 (tm-30) REVERT: O 633 ARG cc_start: 0.9044 (ptt180) cc_final: 0.8711 (ptt90) REVERT: O 638 ASP cc_start: 0.8037 (p0) cc_final: 0.7752 (p0) REVERT: O 642 LYS cc_start: 0.9264 (mttt) cc_final: 0.8297 (tttt) REVERT: P 155 ASP cc_start: 0.9084 (m-30) cc_final: 0.8802 (m-30) REVERT: P 176 PHE cc_start: 0.7404 (m-10) cc_final: 0.6950 (m-10) REVERT: P 289 LEU cc_start: 0.7925 (tp) cc_final: 0.7610 (tp) REVERT: P 333 ASP cc_start: 0.8762 (t0) cc_final: 0.8551 (t0) outliers start: 0 outliers final: 0 residues processed: 2761 average time/residue: 1.4299 time to fit residues: 6441.6304 Evaluate side-chains 2570 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2570 time to evaluate : 6.465 ------------------------------------------------------------------------------- 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: 1.9990 chunk 613 optimal weight: 6.9990 chunk 653 optimal weight: 3.9990 chunk 393 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 513 optimal weight: 0.2980 chunk 200 optimal weight: 2.9990 chunk 590 optimal weight: 2.9990 chunk 618 optimal weight: 8.9990 chunk 651 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 HIS E 27 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 348 HIS ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 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** O 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.7824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 58944 Z= 0.213 Angle : 0.550 7.422 80072 Z= 0.299 Chirality : 0.038 0.356 9440 Planarity : 0.005 0.051 10304 Dihedral : 5.770 54.682 8248 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.25 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.51 (0.10), residues: 7288 helix: 1.19 (0.08), residues: 4056 sheet: -1.34 (0.21), residues: 576 loop : -0.50 (0.13), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 268 HIS 0.014 0.001 HIS J 348 PHE 0.026 0.001 PHE M 374 TYR 0.022 0.002 TYR K 322 ARG 0.014 0.001 ARG L 400 *********************** 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 2744 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2744 time to evaluate : 6.881 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: 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9084 (mp0) REVERT: A 122 ASN cc_start: 0.9135 (t0) cc_final: 0.8905 (t0) REVERT: A 294 MET cc_start: 0.9144 (mmp) cc_final: 0.8692 (mmm) REVERT: A 336 LEU cc_start: 0.9220 (mt) cc_final: 0.8907 (mt) REVERT: A 420 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7845 (mm-40) REVERT: A 429 LEU cc_start: 0.9375 (mm) cc_final: 0.9166 (mm) REVERT: A 444 GLN cc_start: 0.9047 (tp40) cc_final: 0.8604 (tm-30) REVERT: A 453 GLU cc_start: 0.8508 (mp0) cc_final: 0.8154 (mp0) REVERT: A 466 GLU cc_start: 0.8858 (pp20) cc_final: 0.7968 (pp20) REVERT: A 470 CYS cc_start: 0.8105 (m) cc_final: 0.7896 (m) REVERT: A 619 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8687 (tm-30) REVERT: B 155 ASP cc_start: 0.8974 (m-30) cc_final: 0.8734 (m-30) REVERT: B 176 PHE cc_start: 0.7542 (m-10) cc_final: 0.6821 (m-80) REVERT: B 219 ASP cc_start: 0.8155 (t0) cc_final: 0.7823 (t0) REVERT: B 275 LEU cc_start: 0.7389 (mt) cc_final: 0.6593 (mp) REVERT: B 277 CYS cc_start: 0.8539 (p) cc_final: 0.7794 (p) REVERT: B 289 LEU cc_start: 0.7368 (tp) cc_final: 0.7153 (tp) REVERT: B 293 GLN cc_start: 0.7227 (tt0) cc_final: 0.6408 (tp-100) REVERT: B 297 LEU cc_start: 0.8173 (tt) cc_final: 0.7774 (tt) REVERT: C 131 HIS cc_start: 0.8364 (t70) cc_final: 0.8085 (t70) REVERT: C 173 PHE cc_start: 0.8990 (m-80) cc_final: 0.8674 (m-80) REVERT: C 396 ILE cc_start: 0.9396 (pt) cc_final: 0.9179 (tp) REVERT: C 407 PHE cc_start: 0.7022 (p90) cc_final: 0.6495 (p90) REVERT: C 420 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7732 (mm110) REVERT: C 423 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8250 (mtp85) REVERT: C 426 GLU cc_start: 0.8516 (mp0) cc_final: 0.8206 (mp0) REVERT: C 439 MET cc_start: 0.8674 (mmt) cc_final: 0.8429 (mmm) REVERT: C 444 GLN cc_start: 0.9304 (tp40) cc_final: 0.8786 (tm-30) REVERT: C 619 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8847 (tm-30) REVERT: C 620 VAL cc_start: 0.9310 (t) cc_final: 0.8756 (t) REVERT: C 630 LEU cc_start: 0.9496 (mt) cc_final: 0.9265 (mt) REVERT: D 148 LEU cc_start: 0.8613 (mp) cc_final: 0.8163 (tp) REVERT: D 159 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8355 (mt-10) REVERT: D 176 PHE cc_start: 0.7939 (m-10) cc_final: 0.7406 (m-80) REVERT: D 219 ASP cc_start: 0.8444 (t70) cc_final: 0.8123 (t0) REVERT: D 283 MET cc_start: 0.8024 (ppp) cc_final: 0.7724 (ppp) REVERT: D 289 LEU cc_start: 0.7660 (tp) cc_final: 0.7400 (tp) REVERT: E 24 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8774 (mp10) REVERT: E 139 VAL cc_start: 0.9484 (m) cc_final: 0.9167 (p) REVERT: E 220 MET cc_start: 0.6191 (ppp) cc_final: 0.5983 (ppp) REVERT: E 291 ARG cc_start: 0.9457 (mtm110) cc_final: 0.9166 (mtm110) REVERT: E 294 MET cc_start: 0.8711 (mmp) cc_final: 0.8404 (mmm) REVERT: E 295 HIS cc_start: 0.8825 (m-70) cc_final: 0.8491 (m90) REVERT: E 336 LEU cc_start: 0.9249 (mt) cc_final: 0.8930 (mt) REVERT: E 426 GLU cc_start: 0.8535 (mp0) cc_final: 0.8230 (mp0) REVERT: E 466 GLU cc_start: 0.8894 (pp20) cc_final: 0.7985 (pp20) REVERT: E 619 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8756 (tm-30) REVERT: E 633 ARG cc_start: 0.9092 (ptt180) cc_final: 0.8577 (ptt90) REVERT: E 634 LYS cc_start: 0.9491 (ptmt) cc_final: 0.8963 (mmtm) REVERT: F 129 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6950 (tp30) REVERT: F 159 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8790 (mt-10) REVERT: F 176 PHE cc_start: 0.7917 (m-10) cc_final: 0.7569 (m-80) REVERT: F 219 ASP cc_start: 0.8209 (t70) cc_final: 0.7861 (t0) REVERT: F 292 VAL cc_start: 0.7352 (t) cc_final: 0.7032 (t) REVERT: F 293 GLN cc_start: 0.6928 (tp40) cc_final: 0.6718 (tp40) REVERT: G 122 ASN cc_start: 0.8822 (t0) cc_final: 0.8570 (t0) REVERT: G 287 ARG cc_start: 0.9071 (mmt180) cc_final: 0.8562 (mmp-170) REVERT: G 294 MET cc_start: 0.9040 (mmm) cc_final: 0.8776 (mmp) REVERT: G 303 GLU cc_start: 0.8975 (mp0) cc_final: 0.8708 (mp0) REVERT: G 396 ILE cc_start: 0.9238 (pt) cc_final: 0.8941 (tp) REVERT: G 426 GLU cc_start: 0.8333 (mp0) cc_final: 0.8075 (mp0) REVERT: G 466 GLU cc_start: 0.9106 (pp20) cc_final: 0.8146 (pp20) REVERT: G 470 CYS cc_start: 0.8372 (m) cc_final: 0.8026 (m) REVERT: G 473 ARG cc_start: 0.8451 (ptm160) cc_final: 0.8132 (mtm-85) REVERT: G 619 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8748 (tm-30) REVERT: G 633 ARG cc_start: 0.9198 (ptt180) cc_final: 0.8805 (ptt90) REVERT: H 148 LEU cc_start: 0.8652 (mp) cc_final: 0.8382 (mp) REVERT: H 176 PHE cc_start: 0.7953 (m-10) cc_final: 0.7697 (m-80) REVERT: H 219 ASP cc_start: 0.8522 (t0) cc_final: 0.8308 (t0) REVERT: H 289 LEU cc_start: 0.7534 (tp) cc_final: 0.7306 (tp) REVERT: H 422 ASN cc_start: 0.7338 (t0) cc_final: 0.7087 (t0) REVERT: I 15 PHE cc_start: 0.8933 (m-80) cc_final: 0.8589 (m-80) REVERT: I 122 ASN cc_start: 0.9157 (t0) cc_final: 0.8951 (t0) REVERT: I 195 GLU cc_start: 0.8999 (tp30) cc_final: 0.8698 (tp30) REVERT: I 220 MET cc_start: 0.7550 (ttp) cc_final: 0.6702 (ppp) REVERT: I 287 ARG cc_start: 0.8941 (mmt180) cc_final: 0.8739 (mmt180) REVERT: I 294 MET cc_start: 0.9243 (mmp) cc_final: 0.8854 (mmm) REVERT: I 336 LEU cc_start: 0.9236 (mt) cc_final: 0.8932 (mt) REVERT: I 466 GLU cc_start: 0.9025 (pp20) cc_final: 0.8057 (pp20) REVERT: I 467 VAL cc_start: 0.9239 (t) cc_final: 0.8938 (t) REVERT: I 470 CYS cc_start: 0.8679 (m) cc_final: 0.8071 (m) REVERT: I 473 ARG cc_start: 0.8663 (ptp-110) cc_final: 0.8312 (mtm-85) REVERT: I 501 PHE cc_start: 0.8424 (t80) cc_final: 0.8200 (t80) REVERT: I 619 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8944 (tm-30) REVERT: I 620 VAL cc_start: 0.9173 (t) cc_final: 0.8676 (t) REVERT: J 148 LEU cc_start: 0.8727 (mt) cc_final: 0.8395 (tp) REVERT: J 155 ASP cc_start: 0.9214 (t0) cc_final: 0.8888 (t70) REVERT: J 159 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8879 (mt-10) REVERT: J 176 PHE cc_start: 0.7816 (m-10) cc_final: 0.7555 (m-80) REVERT: J 192 ASP cc_start: 0.8277 (m-30) cc_final: 0.7311 (m-30) REVERT: J 219 ASP cc_start: 0.8021 (t70) cc_final: 0.7680 (t0) REVERT: J 256 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8908 (mt-10) REVERT: J 305 VAL cc_start: 0.8446 (t) cc_final: 0.8218 (t) REVERT: K 122 ASN cc_start: 0.8905 (t0) cc_final: 0.8691 (t0) REVERT: K 139 VAL cc_start: 0.9689 (m) cc_final: 0.9411 (p) REVERT: K 150 MET cc_start: 0.7691 (tpp) cc_final: 0.7229 (tpp) REVERT: K 291 ARG cc_start: 0.9473 (mtp-110) cc_final: 0.9162 (mtm110) REVERT: K 295 HIS cc_start: 0.8752 (m90) cc_final: 0.8498 (m90) REVERT: K 324 GLU cc_start: 0.7299 (mp0) cc_final: 0.6927 (mp0) REVERT: K 336 LEU cc_start: 0.9178 (mt) cc_final: 0.8881 (mt) REVERT: K 396 ILE cc_start: 0.9346 (pt) cc_final: 0.9121 (tp) REVERT: K 407 PHE cc_start: 0.6520 (p90) cc_final: 0.6095 (p90) REVERT: K 466 GLU cc_start: 0.8963 (pp20) cc_final: 0.8036 (pp20) REVERT: K 467 VAL cc_start: 0.9149 (t) cc_final: 0.8895 (t) REVERT: K 633 ARG cc_start: 0.9069 (ptt180) cc_final: 0.8774 (ptt90) REVERT: K 710 TRP cc_start: 0.3940 (t-100) cc_final: 0.3575 (t-100) REVERT: L 129 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6845 (tp30) REVERT: L 148 LEU cc_start: 0.8364 (mp) cc_final: 0.7948 (tp) REVERT: L 159 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8289 (mt-10) REVERT: L 176 PHE cc_start: 0.7295 (m-10) cc_final: 0.6782 (m-10) REVERT: L 289 LEU cc_start: 0.7473 (tp) cc_final: 0.7221 (tp) REVERT: L 292 VAL cc_start: 0.7240 (p) cc_final: 0.7019 (p) REVERT: L 399 GLU cc_start: 0.8187 (pm20) cc_final: 0.7957 (pm20) REVERT: M 24 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8661 (mp10) REVERT: M 220 MET cc_start: 0.6775 (tmm) cc_final: 0.6301 (ppp) REVERT: M 287 ARG cc_start: 0.9110 (mmt180) cc_final: 0.8678 (mmm160) REVERT: M 294 MET cc_start: 0.9133 (mmp) cc_final: 0.8780 (mmp) REVERT: M 324 GLU cc_start: 0.7466 (pm20) cc_final: 0.6991 (mp0) REVERT: M 379 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8030 (tm-30) REVERT: M 423 ARG cc_start: 0.9017 (mtp-110) cc_final: 0.8813 (mtp-110) REVERT: M 425 GLU cc_start: 0.8279 (pp20) cc_final: 0.7809 (pp20) REVERT: M 429 LEU cc_start: 0.9446 (mp) cc_final: 0.9009 (mp) REVERT: M 466 GLU cc_start: 0.8910 (pp20) cc_final: 0.8569 (pp20) REVERT: M 467 VAL cc_start: 0.9179 (t) cc_final: 0.8932 (t) REVERT: M 619 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8982 (tm-30) REVERT: M 620 VAL cc_start: 0.9283 (t) cc_final: 0.8828 (t) REVERT: M 630 LEU cc_start: 0.9482 (mt) cc_final: 0.9262 (mt) REVERT: M 638 ASP cc_start: 0.7968 (p0) cc_final: 0.7743 (p0) REVERT: M 642 LYS cc_start: 0.9343 (mttt) cc_final: 0.8540 (tttt) REVERT: M 680 MET cc_start: 0.7925 (tmm) cc_final: 0.7188 (tmm) REVERT: M 684 ARG cc_start: 0.8716 (ptm160) cc_final: 0.8502 (ptm160) REVERT: N 260 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9244 (ttpp) REVERT: O 122 ASN cc_start: 0.8746 (t0) cc_final: 0.8386 (t0) REVERT: O 294 MET cc_start: 0.9091 (mmp) cc_final: 0.8786 (mmm) REVERT: O 441 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8848 (tpp80) REVERT: O 466 GLU cc_start: 0.8949 (pp20) cc_final: 0.7952 (pp20) REVERT: O 470 CYS cc_start: 0.8189 (m) cc_final: 0.7938 (m) REVERT: O 619 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8823 (tm-30) REVERT: O 638 ASP cc_start: 0.8139 (p0) cc_final: 0.7889 (p0) REVERT: O 642 LYS cc_start: 0.9397 (mttt) cc_final: 0.8535 (tttt) REVERT: P 155 ASP cc_start: 0.9070 (m-30) cc_final: 0.8795 (m-30) REVERT: P 176 PHE cc_start: 0.7515 (m-10) cc_final: 0.6949 (m-10) REVERT: P 333 ASP cc_start: 0.8744 (t0) cc_final: 0.8532 (t70) outliers start: 0 outliers final: 0 residues processed: 2744 average time/residue: 1.3939 time to fit residues: 6218.4722 Evaluate side-chains 2541 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2541 time to evaluate : 6.499 ------------------------------------------------------------------------------- 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: 9.9990 chunk 691 optimal weight: 0.0870 chunk 422 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 480 optimal weight: 5.9990 chunk 725 optimal weight: 10.0000 chunk 667 optimal weight: 0.6980 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 HIS ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 444 GLN ** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 58944 Z= 0.204 Angle : 0.546 7.376 80072 Z= 0.296 Chirality : 0.039 0.363 9440 Planarity : 0.005 0.070 10304 Dihedral : 5.781 54.893 8248 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.09 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.48 (0.10), residues: 7288 helix: 1.17 (0.08), residues: 4048 sheet: -1.29 (0.21), residues: 576 loop : -0.54 (0.13), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 268 HIS 0.010 0.001 HIS K 296 PHE 0.030 0.001 PHE O 374 TYR 0.030 0.002 TYR H 444 ARG 0.008 0.001 ARG O 423 ********************** 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 2756 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2756 time to evaluate : 6.757 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: 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9110 (mp0) REVERT: A 122 ASN cc_start: 0.9133 (t0) cc_final: 0.8902 (t0) REVERT: A 336 LEU cc_start: 0.9179 (mt) cc_final: 0.8847 (mt) REVERT: A 429 LEU cc_start: 0.9426 (mm) cc_final: 0.9165 (mm) REVERT: A 444 GLN cc_start: 0.9047 (tp40) cc_final: 0.8594 (tm-30) REVERT: A 466 GLU cc_start: 0.8877 (pp20) cc_final: 0.7995 (pp20) REVERT: A 467 VAL cc_start: 0.9201 (t) cc_final: 0.9000 (t) REVERT: A 470 CYS cc_start: 0.8100 (m) cc_final: 0.7887 (m) REVERT: A 619 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8768 (tm-30) REVERT: B 155 ASP cc_start: 0.8911 (m-30) cc_final: 0.8636 (m-30) REVERT: B 176 PHE cc_start: 0.7571 (m-10) cc_final: 0.6837 (m-80) REVERT: B 219 ASP cc_start: 0.8167 (t0) cc_final: 0.7844 (t0) REVERT: B 275 LEU cc_start: 0.7360 (mt) cc_final: 0.6669 (mp) REVERT: B 277 CYS cc_start: 0.8625 (p) cc_final: 0.7918 (p) REVERT: B 293 GLN cc_start: 0.7360 (tt0) cc_final: 0.6453 (tp-100) REVERT: B 297 LEU cc_start: 0.8141 (tt) cc_final: 0.7734 (tt) REVERT: C 15 PHE cc_start: 0.9007 (m-80) cc_final: 0.8754 (m-80) REVERT: C 110 GLU cc_start: 0.8871 (tt0) cc_final: 0.8551 (tt0) REVERT: C 131 HIS cc_start: 0.8386 (t70) cc_final: 0.8141 (t70) REVERT: C 173 PHE cc_start: 0.9009 (m-80) cc_final: 0.8718 (m-80) REVERT: C 396 ILE cc_start: 0.9403 (pt) cc_final: 0.9185 (tp) REVERT: C 407 PHE cc_start: 0.7122 (p90) cc_final: 0.6583 (p90) REVERT: C 420 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7732 (mm110) REVERT: C 423 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8285 (mtp85) REVERT: C 426 GLU cc_start: 0.8506 (mp0) cc_final: 0.8229 (mp0) REVERT: C 444 GLN cc_start: 0.9307 (tp40) cc_final: 0.8824 (tm-30) REVERT: C 466 GLU cc_start: 0.8903 (pp20) cc_final: 0.8034 (pp20) REVERT: C 470 CYS cc_start: 0.8008 (m) cc_final: 0.7755 (m) REVERT: C 478 VAL cc_start: 0.9105 (t) cc_final: 0.8878 (t) REVERT: C 619 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8825 (tm-30) REVERT: C 620 VAL cc_start: 0.9294 (t) cc_final: 0.8706 (t) REVERT: C 630 LEU cc_start: 0.9482 (mt) cc_final: 0.9267 (mt) REVERT: D 148 LEU cc_start: 0.8562 (mp) cc_final: 0.8129 (tp) REVERT: D 159 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8357 (mt-10) REVERT: D 176 PHE cc_start: 0.7985 (m-10) cc_final: 0.7511 (m-80) REVERT: D 219 ASP cc_start: 0.8482 (t70) cc_final: 0.8163 (t0) REVERT: D 289 LEU cc_start: 0.7516 (tp) cc_final: 0.7222 (tp) REVERT: D 292 VAL cc_start: 0.7708 (p) cc_final: 0.7439 (p) REVERT: E 24 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8785 (mp10) REVERT: E 122 ASN cc_start: 0.8935 (t0) cc_final: 0.8729 (t0) REVERT: E 139 VAL cc_start: 0.9496 (m) cc_final: 0.9096 (p) REVERT: E 291 ARG cc_start: 0.9451 (mtm110) cc_final: 0.9149 (mtm110) REVERT: E 294 MET cc_start: 0.8734 (mmp) cc_final: 0.8475 (mmm) REVERT: E 295 HIS cc_start: 0.8783 (m-70) cc_final: 0.8455 (m90) REVERT: E 336 LEU cc_start: 0.9230 (mt) cc_final: 0.8909 (mt) REVERT: E 339 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8631 (tttp) REVERT: E 426 GLU cc_start: 0.8545 (mp0) cc_final: 0.8228 (mp0) REVERT: E 460 LEU cc_start: 0.8941 (tp) cc_final: 0.8735 (tp) REVERT: E 466 GLU cc_start: 0.8889 (pp20) cc_final: 0.7947 (pp20) REVERT: E 619 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8746 (tm-30) REVERT: E 633 ARG cc_start: 0.9072 (ptt180) cc_final: 0.8574 (ptt90) REVERT: E 634 LYS cc_start: 0.9500 (ptmt) cc_final: 0.8957 (mmtm) REVERT: F 129 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7041 (tp30) REVERT: F 148 LEU cc_start: 0.8798 (tp) cc_final: 0.8508 (tp) REVERT: F 159 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8886 (mt-10) REVERT: F 176 PHE cc_start: 0.8006 (m-10) cc_final: 0.7657 (m-80) REVERT: F 219 ASP cc_start: 0.8180 (t70) cc_final: 0.7853 (t0) REVERT: F 292 VAL cc_start: 0.7300 (t) cc_final: 0.6998 (t) REVERT: F 293 GLN cc_start: 0.6611 (tp40) cc_final: 0.6400 (tp-100) REVERT: G 122 ASN cc_start: 0.8872 (t0) cc_final: 0.8613 (t0) REVERT: G 287 ARG cc_start: 0.9069 (mmt180) cc_final: 0.8563 (mmp-170) REVERT: G 294 MET cc_start: 0.9054 (mmm) cc_final: 0.8772 (mmm) REVERT: G 303 GLU cc_start: 0.8941 (mp0) cc_final: 0.8681 (mp0) REVERT: G 370 PHE cc_start: 0.8196 (m-80) cc_final: 0.7956 (m-80) REVERT: G 396 ILE cc_start: 0.9267 (pt) cc_final: 0.8986 (tp) REVERT: G 466 GLU cc_start: 0.9108 (pp20) cc_final: 0.8109 (pp20) REVERT: G 467 VAL cc_start: 0.9301 (t) cc_final: 0.8959 (t) REVERT: G 470 CYS cc_start: 0.8400 (m) cc_final: 0.8000 (m) REVERT: G 473 ARG cc_start: 0.8451 (ptm160) cc_final: 0.8140 (mtm-85) REVERT: G 619 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8746 (tm-30) REVERT: G 620 VAL cc_start: 0.9219 (t) cc_final: 0.8700 (t) REVERT: G 633 ARG cc_start: 0.9204 (ptt180) cc_final: 0.8743 (ptt90) REVERT: G 634 LYS cc_start: 0.9478 (pttp) cc_final: 0.8875 (mmtm) REVERT: G 710 TRP cc_start: 0.4020 (t-100) cc_final: 0.3593 (t-100) REVERT: H 148 LEU cc_start: 0.8654 (mp) cc_final: 0.8395 (mp) REVERT: H 176 PHE cc_start: 0.7994 (m-10) cc_final: 0.7753 (m-80) REVERT: H 219 ASP cc_start: 0.8543 (t0) cc_final: 0.8313 (t0) REVERT: H 422 ASN cc_start: 0.7137 (t0) cc_final: 0.6881 (t0) REVERT: I 15 PHE cc_start: 0.8946 (m-80) cc_final: 0.8593 (m-80) REVERT: I 131 HIS cc_start: 0.8647 (t70) cc_final: 0.8396 (t70) REVERT: I 195 GLU cc_start: 0.9078 (tp30) cc_final: 0.8669 (tp30) REVERT: I 220 MET cc_start: 0.7543 (ttp) cc_final: 0.6679 (ppp) REVERT: I 287 ARG cc_start: 0.8937 (mmt180) cc_final: 0.8723 (mmt180) REVERT: I 294 MET cc_start: 0.9262 (mmp) cc_final: 0.8895 (mmm) REVERT: I 336 LEU cc_start: 0.9226 (mt) cc_final: 0.8904 (mt) REVERT: I 466 GLU cc_start: 0.9013 (pp20) cc_final: 0.8003 (pp20) REVERT: I 467 VAL cc_start: 0.9242 (t) cc_final: 0.8951 (t) REVERT: I 470 CYS cc_start: 0.8659 (m) cc_final: 0.8061 (m) REVERT: I 473 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8325 (mtm-85) REVERT: I 501 PHE cc_start: 0.8479 (t80) cc_final: 0.8243 (t80) REVERT: I 619 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8936 (tm-30) REVERT: I 620 VAL cc_start: 0.9217 (t) cc_final: 0.8732 (t) REVERT: J 155 ASP cc_start: 0.9136 (t0) cc_final: 0.8845 (t70) REVERT: J 159 GLU cc_start: 0.9433 (mm-30) cc_final: 0.8933 (mt-10) REVERT: J 176 PHE cc_start: 0.7868 (m-10) cc_final: 0.7625 (m-80) REVERT: J 219 ASP cc_start: 0.8039 (t70) cc_final: 0.7698 (t0) REVERT: J 256 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8917 (mt-10) REVERT: K 122 ASN cc_start: 0.8876 (t0) cc_final: 0.8626 (t0) REVERT: K 139 VAL cc_start: 0.9692 (m) cc_final: 0.9371 (p) REVERT: K 150 MET cc_start: 0.7594 (tpp) cc_final: 0.7121 (tpp) REVERT: K 291 ARG cc_start: 0.9469 (mtp-110) cc_final: 0.9165 (mtm110) REVERT: K 295 HIS cc_start: 0.8778 (m90) cc_final: 0.8503 (m90) REVERT: K 324 GLU cc_start: 0.7301 (mp0) cc_final: 0.6946 (mp0) REVERT: K 336 LEU cc_start: 0.9215 (mt) cc_final: 0.8890 (mt) REVERT: K 396 ILE cc_start: 0.9352 (pt) cc_final: 0.9131 (tp) REVERT: K 423 ARG cc_start: 0.8839 (mtt90) cc_final: 0.8518 (ttm110) REVERT: K 466 GLU cc_start: 0.8949 (pp20) cc_final: 0.8024 (pp20) REVERT: K 467 VAL cc_start: 0.9140 (t) cc_final: 0.8882 (t) REVERT: K 633 ARG cc_start: 0.9071 (ptt180) cc_final: 0.8568 (ptt90) REVERT: K 634 LYS cc_start: 0.9512 (ptmt) cc_final: 0.8977 (mmtm) REVERT: K 710 TRP cc_start: 0.4334 (t-100) cc_final: 0.3634 (t-100) REVERT: L 129 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6833 (tp30) REVERT: L 148 LEU cc_start: 0.8398 (mp) cc_final: 0.7976 (tp) REVERT: L 159 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8318 (mt-10) REVERT: L 289 LEU cc_start: 0.7456 (tp) cc_final: 0.7192 (tp) REVERT: L 292 VAL cc_start: 0.7222 (p) cc_final: 0.7015 (p) REVERT: M 110 GLU cc_start: 0.8405 (tt0) cc_final: 0.8188 (tt0) REVERT: M 140 VAL cc_start: 0.9565 (m) cc_final: 0.9317 (m) REVERT: M 220 MET cc_start: 0.6784 (tmm) cc_final: 0.6318 (ppp) REVERT: M 287 ARG cc_start: 0.9125 (mmt180) cc_final: 0.8652 (mmm160) REVERT: M 294 MET cc_start: 0.9162 (mmp) cc_final: 0.8697 (mmp) REVERT: M 324 GLU cc_start: 0.7530 (pm20) cc_final: 0.7220 (mp0) REVERT: M 336 LEU cc_start: 0.9243 (mt) cc_final: 0.8984 (mt) REVERT: M 379 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7991 (tm-30) REVERT: M 423 ARG cc_start: 0.9055 (mtp-110) cc_final: 0.8824 (mtp-110) REVERT: M 425 GLU cc_start: 0.8312 (pp20) cc_final: 0.7846 (pp20) REVERT: M 429 LEU cc_start: 0.9462 (mp) cc_final: 0.8994 (mp) REVERT: M 466 GLU cc_start: 0.8864 (pp20) cc_final: 0.8513 (pp20) REVERT: M 467 VAL cc_start: 0.9173 (t) cc_final: 0.8927 (t) REVERT: M 619 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8931 (tm-30) REVERT: M 620 VAL cc_start: 0.9276 (t) cc_final: 0.8907 (t) REVERT: M 630 LEU cc_start: 0.9488 (mt) cc_final: 0.9267 (mt) REVERT: M 638 ASP cc_start: 0.7742 (p0) cc_final: 0.7532 (p0) REVERT: M 642 LYS cc_start: 0.9356 (mttt) cc_final: 0.8523 (tttt) REVERT: M 645 MET cc_start: 0.6642 (ttp) cc_final: 0.6397 (ttp) REVERT: M 684 ARG cc_start: 0.8797 (ptm160) cc_final: 0.8360 (ptm160) REVERT: N 260 LYS cc_start: 0.9470 (ttpp) cc_final: 0.9218 (ttpp) REVERT: N 268 TRP cc_start: 0.8661 (m100) cc_final: 0.8308 (m100) REVERT: O 122 ASN cc_start: 0.8804 (t0) cc_final: 0.8461 (t0) REVERT: O 278 ASN cc_start: 0.6839 (p0) cc_final: 0.6617 (p0) REVERT: O 294 MET cc_start: 0.9080 (mmp) cc_final: 0.8723 (mmm) REVERT: O 441 ARG cc_start: 0.9133 (mmm-85) cc_final: 0.8864 (tpp80) REVERT: O 460 LEU cc_start: 0.9181 (tp) cc_final: 0.8948 (tp) REVERT: O 466 GLU cc_start: 0.8957 (pp20) cc_final: 0.7952 (pp20) REVERT: O 467 VAL cc_start: 0.9129 (m) cc_final: 0.8674 (m) REVERT: O 470 CYS cc_start: 0.8354 (m) cc_final: 0.8122 (m) REVERT: O 618 CYS cc_start: 0.8744 (t) cc_final: 0.8466 (t) REVERT: O 619 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8889 (tm-30) REVERT: O 620 VAL cc_start: 0.9270 (t) cc_final: 0.8823 (t) REVERT: O 638 ASP cc_start: 0.8018 (p0) cc_final: 0.7765 (p0) REVERT: O 642 LYS cc_start: 0.9351 (mttt) cc_final: 0.8396 (tttt) REVERT: O 673 LEU cc_start: 0.8517 (mt) cc_final: 0.8310 (mt) REVERT: P 155 ASP cc_start: 0.9091 (m-30) cc_final: 0.8813 (m-30) REVERT: P 176 PHE cc_start: 0.7551 (m-10) cc_final: 0.6924 (m-10) REVERT: P 289 LEU cc_start: 0.7846 (tp) cc_final: 0.7601 (tp) outliers start: 0 outliers final: 0 residues processed: 2756 average time/residue: 1.3995 time to fit residues: 6310.5235 Evaluate side-chains 2554 residues out of total 6368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2554 time to evaluate : 6.475 ------------------------------------------------------------------------------- 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: 10.0000 chunk 615 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 532 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 578 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN ** I 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 HIS ** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 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** O 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.140734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.090960 restraints weight = 392823.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097196 restraints weight = 187781.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101326 restraints weight = 111383.867| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 58944 Z= 0.164 Angle : 0.516 7.374 80072 Z= 0.273 Chirality : 0.039 0.361 9440 Planarity : 0.005 0.051 10304 Dihedral : 5.677 54.759 8248 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.73 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.83 (0.10), residues: 7288 helix: 1.46 (0.08), residues: 4064 sheet: -1.16 (0.21), residues: 576 loop : -0.39 (0.13), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP P 268 HIS 0.007 0.001 HIS K 296 PHE 0.028 0.001 PHE I 374 TYR 0.018 0.001 TYR I 322 ARG 0.008 0.001 ARG J 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 73686.39 seconds wall clock time: 1251 minutes 50.57 seconds (75110.57 seconds total)