Starting phenix.real_space_refine on Mon Mar 18 03:10:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzw_8188/03_2024/5jzw_8188.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzw_8188/03_2024/5jzw_8188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzw_8188/03_2024/5jzw_8188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzw_8188/03_2024/5jzw_8188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzw_8188/03_2024/5jzw_8188.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzw_8188/03_2024/5jzw_8188.pdb" } resolution = 4.46 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= 0.003 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 27055 2.51 5 N 7434 2.21 5 O 8295 1.98 5 H 40509 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 83419 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 5801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5801 Classifications: {'peptide': 381} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Chain: "I" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Chain: "J" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Chain: "K" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Chain: "L" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Chain: "M" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Chain: "N" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6116 Classifications: {'peptide': 401} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PTRANS': 23, 'TRANS': 374} Chain breaks: 1 Time building chain proxies: 27.47, per 1000 atoms: 0.33 Number of scatterers: 83419 At special positions: 0 Unit cell: (176.88, 179.56, 152.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 8295 8.00 N 7434 7.00 C 27055 6.00 H 40509 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 75 " distance=2.14 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 164 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 75 " distance=2.14 Simple disulfide: pdb=" SG CYS I 159 " - pdb=" SG CYS I 164 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 75 " distance=2.14 Simple disulfide: pdb=" SG CYS J 159 " - pdb=" SG CYS J 164 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 75 " distance=2.14 Simple disulfide: pdb=" SG CYS K 159 " - pdb=" SG CYS K 164 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 75 " distance=2.14 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 164 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 75 " distance=2.14 Simple disulfide: pdb=" SG CYS M 159 " - pdb=" SG CYS M 164 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 75 " distance=2.14 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.70 Conformation dependent library (CDL) restraints added in 6.2 seconds 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9828 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 0 sheets defined 21.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.501A pdb=" N SER A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.854A pdb=" N TYR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 363 removed outlier: 4.316A pdb=" N TYR A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.502A pdb=" N SER B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.853A pdb=" N TYR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 355 through 363 removed outlier: 4.315A pdb=" N TYR B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 381 Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.500A pdb=" N SER C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.853A pdb=" N TYR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 355 through 363 removed outlier: 4.315A pdb=" N TYR C 363 " --> pdb=" O TRP C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.501A pdb=" N SER D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.852A pdb=" N TYR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 Processing helix chain 'D' and resid 355 through 363 removed outlier: 4.316A pdb=" N TYR D 363 " --> pdb=" O TRP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 381 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.502A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 124 removed outlier: 3.852A pdb=" N TYR E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 Processing helix chain 'E' and resid 355 through 363 removed outlier: 4.316A pdb=" N TYR E 363 " --> pdb=" O TRP E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 381 Processing helix chain 'E' and resid 385 through 393 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 27 through 34 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 99 through 109 removed outlier: 3.502A pdb=" N SER F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 124 removed outlier: 3.852A pdb=" N TYR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 Processing helix chain 'F' and resid 355 through 363 removed outlier: 4.316A pdb=" N TYR F 363 " --> pdb=" O TRP F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 381 Processing helix chain 'F' and resid 385 through 393 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 99 through 109 removed outlier: 3.500A pdb=" N SER G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 124 removed outlier: 3.853A pdb=" N TYR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 354 Processing helix chain 'G' and resid 355 through 363 removed outlier: 4.315A pdb=" N TYR G 363 " --> pdb=" O TRP G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 381 Processing helix chain 'G' and resid 385 through 393 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 30 through 35 Processing helix chain 'H' and resid 36 through 42 removed outlier: 3.572A pdb=" N GLY H 40 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 62 Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 108 through 111 Processing helix chain 'H' and resid 112 through 124 removed outlier: 3.708A pdb=" N THR H 116 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 Processing helix chain 'H' and resid 354 through 359 removed outlier: 3.670A pdb=" N TRP H 359 " --> pdb=" O ILE H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 362 No H-bonds generated for 'chain 'H' and resid 360 through 362' Processing helix chain 'H' and resid 372 through 381 Processing helix chain 'H' and resid 381 through 394 removed outlier: 3.769A pdb=" N ALA H 390 " --> pdb=" O GLN H 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 30 through 35 Processing helix chain 'I' and resid 36 through 42 removed outlier: 3.574A pdb=" N GLY I 40 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'I' and resid 98 through 107 Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 112 through 124 removed outlier: 3.707A pdb=" N THR I 116 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 353 Processing helix chain 'I' and resid 354 through 359 removed outlier: 3.670A pdb=" N TRP I 359 " --> pdb=" O ILE I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 362 No H-bonds generated for 'chain 'I' and resid 360 through 362' Processing helix chain 'I' and resid 372 through 381 Processing helix chain 'I' and resid 381 through 394 removed outlier: 3.769A pdb=" N ALA I 390 " --> pdb=" O GLN I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 30 through 35 Processing helix chain 'J' and resid 36 through 42 removed outlier: 3.574A pdb=" N GLY J 40 " --> pdb=" O ASN J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 98 through 107 Processing helix chain 'J' and resid 108 through 111 Processing helix chain 'J' and resid 112 through 124 removed outlier: 3.707A pdb=" N THR J 116 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 353 Processing helix chain 'J' and resid 354 through 359 removed outlier: 3.670A pdb=" N TRP J 359 " --> pdb=" O ILE J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 372 through 381 Processing helix chain 'J' and resid 381 through 394 removed outlier: 3.769A pdb=" N ALA J 390 " --> pdb=" O GLN J 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 30 through 35 Processing helix chain 'K' and resid 36 through 42 removed outlier: 3.573A pdb=" N GLY K 40 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 98 through 107 Processing helix chain 'K' and resid 108 through 111 Processing helix chain 'K' and resid 112 through 124 removed outlier: 3.707A pdb=" N THR K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 353 Processing helix chain 'K' and resid 354 through 359 removed outlier: 3.669A pdb=" N TRP K 359 " --> pdb=" O ILE K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 372 through 381 Processing helix chain 'K' and resid 381 through 394 removed outlier: 3.768A pdb=" N ALA K 390 " --> pdb=" O GLN K 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 30 through 35 Processing helix chain 'L' and resid 36 through 42 removed outlier: 3.572A pdb=" N GLY L 40 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 62 Processing helix chain 'L' and resid 98 through 107 Processing helix chain 'L' and resid 108 through 111 Processing helix chain 'L' and resid 112 through 124 removed outlier: 3.708A pdb=" N THR L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 353 Processing helix chain 'L' and resid 354 through 359 removed outlier: 3.669A pdb=" N TRP L 359 " --> pdb=" O ILE L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 362 No H-bonds generated for 'chain 'L' and resid 360 through 362' Processing helix chain 'L' and resid 372 through 381 Processing helix chain 'L' and resid 381 through 394 removed outlier: 3.769A pdb=" N ALA L 390 " --> pdb=" O GLN L 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 30 through 35 Processing helix chain 'M' and resid 36 through 42 removed outlier: 3.572A pdb=" N GLY M 40 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 62 Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 124 removed outlier: 3.708A pdb=" N THR M 116 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 353 Processing helix chain 'M' and resid 354 through 359 removed outlier: 3.668A pdb=" N TRP M 359 " --> pdb=" O ILE M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 360 through 362 No H-bonds generated for 'chain 'M' and resid 360 through 362' Processing helix chain 'M' and resid 372 through 381 Processing helix chain 'M' and resid 381 through 394 removed outlier: 3.769A pdb=" N ALA M 390 " --> pdb=" O GLN M 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 30 through 35 Processing helix chain 'N' and resid 36 through 42 removed outlier: 3.573A pdb=" N GLY N 40 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 62 Processing helix chain 'N' and resid 98 through 107 Processing helix chain 'N' and resid 108 through 111 Processing helix chain 'N' and resid 112 through 124 removed outlier: 3.707A pdb=" N THR N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 353 Processing helix chain 'N' and resid 354 through 359 removed outlier: 3.670A pdb=" N TRP N 359 " --> pdb=" O ILE N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 362 No H-bonds generated for 'chain 'N' and resid 360 through 362' Processing helix chain 'N' and resid 372 through 381 Processing helix chain 'N' and resid 381 through 394 removed outlier: 3.769A pdb=" N ALA N 390 " --> pdb=" O GLN N 386 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1428 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: 21.23 Time building geometry restraints manager: 53.56 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: 40509 1.13 - 1.30: 7276 1.30 - 1.47: 19007 1.47 - 1.65: 17663 1.65 - 1.82: 196 Bond restraints: 84651 Sorted by residual: bond pdb=" N ALA L 424 " pdb=" H ALA L 424 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N ALA I 424 " pdb=" H ALA I 424 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N ALA K 424 " pdb=" H ALA K 424 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ALA H 424 " pdb=" H ALA H 424 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ALA J 424 " pdb=" H ALA J 424 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 84646 not shown) Histogram of bond angle deviations from ideal: 95.15 - 102.95: 171 102.95 - 110.75: 83848 110.75 - 118.55: 25299 118.55 - 126.34: 41480 126.34 - 134.14: 1284 Bond angle restraints: 152082 Sorted by residual: angle pdb=" C GLY E 58 " pdb=" N PRO E 59 " pdb=" CA PRO E 59 " ideal model delta sigma weight residual 119.32 130.63 -11.31 1.14e+00 7.69e-01 9.84e+01 angle pdb=" C GLY G 58 " pdb=" N PRO G 59 " pdb=" CA PRO G 59 " ideal model delta sigma weight residual 119.32 130.60 -11.28 1.14e+00 7.69e-01 9.79e+01 angle pdb=" C GLY F 58 " pdb=" N PRO F 59 " pdb=" CA PRO F 59 " ideal model delta sigma weight residual 119.32 130.60 -11.28 1.14e+00 7.69e-01 9.79e+01 angle pdb=" C GLY C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.32 130.58 -11.26 1.14e+00 7.69e-01 9.76e+01 angle pdb=" C GLY B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 119.32 130.55 -11.23 1.14e+00 7.69e-01 9.71e+01 ... (remaining 152077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 37746 17.07 - 34.13: 1572 34.13 - 51.20: 757 51.20 - 68.26: 322 68.26 - 85.33: 21 Dihedral angle restraints: 40418 sinusoidal: 21518 harmonic: 18900 Sorted by residual: dihedral pdb=" CA TYR M 306 " pdb=" C TYR M 306 " pdb=" N GLU M 307 " pdb=" CA GLU M 307 " ideal model delta harmonic sigma weight residual 0.00 41.01 -41.01 0 5.00e+00 4.00e-02 6.73e+01 dihedral pdb=" CA TYR L 306 " pdb=" C TYR L 306 " pdb=" N GLU L 307 " pdb=" CA GLU L 307 " ideal model delta harmonic sigma weight residual 0.00 41.01 -41.01 0 5.00e+00 4.00e-02 6.73e+01 dihedral pdb=" CA TYR N 306 " pdb=" C TYR N 306 " pdb=" N GLU N 307 " pdb=" CA GLU N 307 " ideal model delta harmonic sigma weight residual 0.00 40.93 -40.93 0 5.00e+00 4.00e-02 6.70e+01 ... (remaining 40415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3151 0.058 - 0.116: 2011 0.116 - 0.174: 814 0.174 - 0.232: 208 0.232 - 0.289: 67 Chirality restraints: 6251 Sorted by residual: chirality pdb=" CA TRP D 373 " pdb=" N TRP D 373 " pdb=" C TRP D 373 " pdb=" CB TRP D 373 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA TRP F 373 " pdb=" N TRP F 373 " pdb=" C TRP F 373 " pdb=" CB TRP F 373 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA TRP B 373 " pdb=" N TRP B 373 " pdb=" C TRP B 373 " pdb=" CB TRP B 373 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 6248 not shown) Planarity restraints: 13048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 270 " 0.073 2.00e-02 2.50e+03 1.31e-01 1.71e+02 pdb=" N GLY H 271 " -0.226 2.00e-02 2.50e+03 pdb=" CA GLY H 271 " 0.064 2.00e-02 2.50e+03 pdb=" H GLY H 271 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY L 270 " 0.073 2.00e-02 2.50e+03 1.31e-01 1.71e+02 pdb=" N GLY L 271 " -0.226 2.00e-02 2.50e+03 pdb=" CA GLY L 271 " 0.064 2.00e-02 2.50e+03 pdb=" H GLY L 271 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 270 " -0.073 2.00e-02 2.50e+03 1.30e-01 1.70e+02 pdb=" N GLY J 271 " 0.225 2.00e-02 2.50e+03 pdb=" CA GLY J 271 " -0.064 2.00e-02 2.50e+03 pdb=" H GLY J 271 " -0.088 2.00e-02 2.50e+03 ... (remaining 13045 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.40: 56 1.40 - 2.20: 11716 2.20 - 3.00: 227761 3.00 - 3.80: 352149 3.80 - 4.60: 566489 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1158171 Sorted by model distance: nonbonded pdb="HD21 ASN E 335 " pdb=" HG2 PRO N 333 " model vdw 0.600 2.270 nonbonded pdb="HD21 ASN D 335 " pdb=" HG2 PRO H 333 " model vdw 0.602 2.270 nonbonded pdb="HD21 ASN F 335 " pdb=" HG2 PRO M 333 " model vdw 0.602 2.270 nonbonded pdb="HD21 ASN G 335 " pdb=" HG2 PRO L 333 " model vdw 0.602 2.270 nonbonded pdb="HD21 ASN C 335 " pdb=" HG2 PRO I 333 " model vdw 0.604 2.270 ... (remaining 1158166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) selection = (chain 'I' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) selection = (chain 'J' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) selection = (chain 'K' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) selection = (chain 'L' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) selection = (chain 'M' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) selection = (chain 'N' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 222 through 226 or resid 270 throu \ gh 424)) } 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: 0.440 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: 1.030 Extract box with map and model: 5.240 Check model and map are aligned: 0.910 Set scattering table: 0.580 Process input model: 185.260 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.250 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 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 : 0.015 0.063 44142 Z= 1.000 Angle : 1.850 17.882 60277 Z= 1.193 Chirality : 0.086 0.289 6251 Planarity : 0.020 0.224 7924 Dihedral : 10.605 85.329 15659 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 5.94 % Allowed : 10.63 % Favored : 83.43 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 5418 helix: -2.59 (0.14), residues: 791 sheet: -0.72 (0.13), residues: 1666 loop : -2.53 (0.10), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.008 TRP F 371 HIS 0.009 0.002 HIS I 341 PHE 0.039 0.005 PHE C 308 TYR 0.046 0.008 TYR J 330 ARG 0.005 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 2009 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2009 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 THR cc_start: 0.4354 (p) cc_final: 0.3866 (p) REVERT: A 388 ASN cc_start: 0.8777 (m-40) cc_final: 0.8154 (m110) REVERT: A 404 PHE cc_start: 0.6400 (t80) cc_final: 0.6080 (t80) REVERT: B 26 VAL cc_start: 0.8872 (t) cc_final: 0.8668 (t) REVERT: B 100 ASP cc_start: 0.8530 (m-30) cc_final: 0.8177 (t0) REVERT: B 151 ILE cc_start: 0.8895 (mt) cc_final: 0.8643 (mt) REVERT: B 331 THR cc_start: 0.5054 (p) cc_final: 0.4595 (p) REVERT: B 379 GLN cc_start: 0.8821 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 384 THR cc_start: 0.8045 (p) cc_final: 0.7338 (p) REVERT: B 388 ASN cc_start: 0.8634 (m-40) cc_final: 0.8095 (m110) REVERT: B 404 PHE cc_start: 0.6859 (t80) cc_final: 0.6497 (t80) REVERT: B 414 ILE cc_start: 0.9312 (mm) cc_final: 0.9093 (mp) REVERT: C 38 ILE cc_start: 0.8793 (pt) cc_final: 0.8450 (pt) REVERT: C 151 ILE cc_start: 0.8673 (mt) cc_final: 0.8408 (mt) REVERT: C 215 TYR cc_start: 0.8194 (m-80) cc_final: 0.7565 (m-80) REVERT: C 308 PHE cc_start: 0.8082 (t80) cc_final: 0.7827 (t80) REVERT: C 331 THR cc_start: 0.5039 (p) cc_final: 0.4406 (p) REVERT: C 379 GLN cc_start: 0.8838 (tp40) cc_final: 0.8237 (tp40) REVERT: C 408 SER cc_start: 0.8838 (p) cc_final: 0.8557 (p) REVERT: D 38 ILE cc_start: 0.8814 (pt) cc_final: 0.8441 (pt) REVERT: D 100 ASP cc_start: 0.8599 (m-30) cc_final: 0.8117 (t0) REVERT: D 331 THR cc_start: 0.4543 (p) cc_final: 0.4021 (p) REVERT: D 379 GLN cc_start: 0.8826 (tp40) cc_final: 0.8238 (tp40) REVERT: D 384 THR cc_start: 0.7951 (p) cc_final: 0.7182 (p) REVERT: D 404 PHE cc_start: 0.6159 (t80) cc_final: 0.5750 (t80) REVERT: E 38 ILE cc_start: 0.9023 (pt) cc_final: 0.8668 (pt) REVERT: E 100 ASP cc_start: 0.8694 (m-30) cc_final: 0.8355 (t0) REVERT: E 151 ILE cc_start: 0.8738 (mt) cc_final: 0.8362 (mt) REVERT: E 188 ASP cc_start: 0.7763 (m-30) cc_final: 0.7515 (p0) REVERT: E 331 THR cc_start: 0.4443 (p) cc_final: 0.3821 (p) REVERT: E 384 THR cc_start: 0.7858 (p) cc_final: 0.6905 (p) REVERT: E 388 ASN cc_start: 0.8699 (m-40) cc_final: 0.8115 (m110) REVERT: E 403 ASP cc_start: 0.7563 (m-30) cc_final: 0.6823 (m-30) REVERT: F 38 ILE cc_start: 0.8944 (pt) cc_final: 0.8501 (pt) REVERT: F 100 ASP cc_start: 0.8646 (m-30) cc_final: 0.8389 (t0) REVERT: F 151 ILE cc_start: 0.8698 (mt) cc_final: 0.8391 (mt) REVERT: F 188 ASP cc_start: 0.7686 (m-30) cc_final: 0.7410 (p0) REVERT: F 331 THR cc_start: 0.4861 (p) cc_final: 0.4287 (p) REVERT: F 403 ASP cc_start: 0.7748 (m-30) cc_final: 0.7015 (m-30) REVERT: F 404 PHE cc_start: 0.7005 (t80) cc_final: 0.6531 (t80) REVERT: G 42 MET cc_start: 0.7435 (mmm) cc_final: 0.7131 (mmm) REVERT: G 82 THR cc_start: 0.5025 (p) cc_final: 0.4781 (p) REVERT: G 188 ASP cc_start: 0.7898 (m-30) cc_final: 0.7608 (p0) REVERT: G 195 GLN cc_start: 0.8372 (pt0) cc_final: 0.8164 (pm20) REVERT: G 288 ARG cc_start: 0.7373 (ptt180) cc_final: 0.7140 (ptt180) REVERT: G 334 ASP cc_start: 0.6882 (p0) cc_final: 0.6332 (p0) REVERT: G 358 GLN cc_start: 0.8450 (mt0) cc_final: 0.8095 (mt0) REVERT: G 371 TRP cc_start: 0.3746 (p90) cc_final: 0.3364 (p90) REVERT: G 379 GLN cc_start: 0.9011 (tp40) cc_final: 0.8594 (tp40) REVERT: G 384 THR cc_start: 0.7744 (p) cc_final: 0.6718 (p) REVERT: H 22 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7667 (mmtm) REVERT: H 41 MET cc_start: 0.9120 (mmm) cc_final: 0.8071 (mmt) REVERT: H 144 ARG cc_start: 0.8304 (ttt180) cc_final: 0.7986 (ttt-90) REVERT: H 170 ILE cc_start: 0.8403 (mt) cc_final: 0.8170 (mt) REVERT: H 175 PHE cc_start: 0.8132 (p90) cc_final: 0.7697 (p90) REVERT: H 185 LYS cc_start: 0.8471 (tttt) cc_final: 0.8130 (mmmt) REVERT: H 203 TRP cc_start: 0.7995 (p90) cc_final: 0.7252 (p90) REVERT: H 213 SER cc_start: 0.8883 (t) cc_final: 0.8591 (p) REVERT: H 376 THR cc_start: 0.9169 (p) cc_final: 0.8952 (p) REVERT: H 380 ASN cc_start: 0.8068 (m-40) cc_final: 0.7633 (t160) REVERT: H 384 THR cc_start: 0.8784 (m) cc_final: 0.7791 (p) REVERT: H 393 LEU cc_start: 0.9159 (mt) cc_final: 0.8438 (tt) REVERT: I 143 THR cc_start: 0.9221 (t) cc_final: 0.8931 (p) REVERT: I 150 VAL cc_start: 0.9054 (t) cc_final: 0.8566 (p) REVERT: I 170 ILE cc_start: 0.8380 (mt) cc_final: 0.8087 (mt) REVERT: I 213 SER cc_start: 0.8397 (t) cc_final: 0.8100 (p) REVERT: I 344 VAL cc_start: 0.9438 (t) cc_final: 0.9199 (t) REVERT: I 376 THR cc_start: 0.9150 (p) cc_final: 0.8821 (p) REVERT: I 379 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8399 (tp40) REVERT: I 380 ASN cc_start: 0.7994 (m-40) cc_final: 0.7743 (t160) REVERT: I 384 THR cc_start: 0.8859 (m) cc_final: 0.8444 (p) REVERT: I 388 ASN cc_start: 0.7457 (m-40) cc_final: 0.7163 (m-40) REVERT: I 393 LEU cc_start: 0.9282 (mt) cc_final: 0.8387 (tt) REVERT: I 396 VAL cc_start: 0.9435 (t) cc_final: 0.9179 (t) REVERT: J 12 PHE cc_start: 0.7389 (m-80) cc_final: 0.7174 (m-80) REVERT: J 116 THR cc_start: 0.9635 (m) cc_final: 0.9414 (p) REVERT: J 170 ILE cc_start: 0.8573 (mt) cc_final: 0.8353 (mt) REVERT: J 185 LYS cc_start: 0.8485 (tttt) cc_final: 0.8085 (mmmt) REVERT: J 203 TRP cc_start: 0.8101 (p90) cc_final: 0.7356 (p90) REVERT: J 213 SER cc_start: 0.8294 (t) cc_final: 0.7974 (p) REVERT: J 216 ASP cc_start: 0.8099 (m-30) cc_final: 0.7881 (t0) REVERT: J 376 THR cc_start: 0.9109 (p) cc_final: 0.8806 (p) REVERT: J 384 THR cc_start: 0.8836 (m) cc_final: 0.8487 (p) REVERT: J 393 LEU cc_start: 0.9187 (mt) cc_final: 0.8469 (tt) REVERT: J 403 ASP cc_start: 0.7627 (p0) cc_final: 0.7422 (p0) REVERT: J 415 GLU cc_start: 0.8565 (pt0) cc_final: 0.8177 (mt-10) REVERT: K 12 PHE cc_start: 0.7616 (m-80) cc_final: 0.7175 (m-80) REVERT: K 41 MET cc_start: 0.9189 (mmm) cc_final: 0.8834 (mmm) REVERT: K 170 ILE cc_start: 0.8312 (mt) cc_final: 0.7980 (mt) REVERT: K 185 LYS cc_start: 0.8409 (tttt) cc_final: 0.8143 (mmpt) REVERT: K 213 SER cc_start: 0.8441 (t) cc_final: 0.8143 (p) REVERT: K 344 VAL cc_start: 0.9541 (t) cc_final: 0.9229 (p) REVERT: K 384 THR cc_start: 0.8653 (m) cc_final: 0.8245 (p) REVERT: K 393 LEU cc_start: 0.9106 (mt) cc_final: 0.8089 (tt) REVERT: K 396 VAL cc_start: 0.9485 (t) cc_final: 0.9265 (t) REVERT: L 22 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7433 (mmtm) REVERT: L 41 MET cc_start: 0.9167 (mmm) cc_final: 0.8949 (mmm) REVERT: L 185 LYS cc_start: 0.8279 (tttt) cc_final: 0.7903 (mmmt) REVERT: L 195 GLN cc_start: 0.8720 (tp40) cc_final: 0.8508 (tp-100) REVERT: L 213 SER cc_start: 0.8634 (t) cc_final: 0.8197 (p) REVERT: L 315 ASP cc_start: 0.7034 (m-30) cc_final: 0.6649 (m-30) REVERT: L 344 VAL cc_start: 0.9504 (t) cc_final: 0.9245 (t) REVERT: L 379 GLN cc_start: 0.8848 (mm-40) cc_final: 0.7946 (tt0) REVERT: L 396 VAL cc_start: 0.9439 (t) cc_final: 0.9148 (t) REVERT: M 12 PHE cc_start: 0.7472 (m-80) cc_final: 0.7074 (m-80) REVERT: M 22 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7590 (mmtt) REVERT: M 41 MET cc_start: 0.9170 (mmm) cc_final: 0.8932 (mmm) REVERT: M 170 ILE cc_start: 0.8452 (mt) cc_final: 0.8188 (mm) REVERT: M 185 LYS cc_start: 0.8474 (tttt) cc_final: 0.8038 (mmmt) REVERT: M 203 TRP cc_start: 0.8060 (p90) cc_final: 0.7245 (p90) REVERT: M 213 SER cc_start: 0.8499 (t) cc_final: 0.8139 (p) REVERT: M 306 TYR cc_start: 0.7601 (m-80) cc_final: 0.7045 (m-10) REVERT: M 358 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8791 (mm-40) REVERT: M 376 THR cc_start: 0.9259 (p) cc_final: 0.9025 (p) REVERT: M 380 ASN cc_start: 0.8055 (m-40) cc_final: 0.7672 (t160) REVERT: M 384 THR cc_start: 0.8652 (m) cc_final: 0.8369 (p) REVERT: M 396 VAL cc_start: 0.9591 (t) cc_final: 0.9230 (t) REVERT: N 41 MET cc_start: 0.9205 (mmm) cc_final: 0.8749 (mmm) REVERT: N 170 ILE cc_start: 0.8479 (mt) cc_final: 0.8243 (mt) REVERT: N 213 SER cc_start: 0.8489 (t) cc_final: 0.8198 (p) REVERT: N 344 VAL cc_start: 0.9412 (t) cc_final: 0.9108 (t) REVERT: N 358 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8764 (mm-40) REVERT: N 376 THR cc_start: 0.9278 (p) cc_final: 0.9073 (p) REVERT: N 379 GLN cc_start: 0.8931 (mm-40) cc_final: 0.7537 (tm-30) REVERT: N 380 ASN cc_start: 0.8072 (m-40) cc_final: 0.6829 (m-40) REVERT: N 384 THR cc_start: 0.8692 (m) cc_final: 0.8153 (p) REVERT: N 393 LEU cc_start: 0.9265 (mt) cc_final: 0.8390 (tt) outliers start: 0 outliers final: 0 residues processed: 2009 average time/residue: 1.1425 time to fit residues: 3645.5646 Evaluate side-chains 1281 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1281 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 461 optimal weight: 1.9990 chunk 413 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 427 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 495 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 340 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 340 ASN ** F 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 ASN H 268 GLN H 388 ASN I 52 ASN I 268 GLN I 380 ASN J 52 ASN J 231 ASN J 268 GLN J 388 ASN K 268 GLN K 388 ASN L 268 GLN M 231 ASN M 268 GLN N 268 GLN N 388 ASN N 409 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 44142 Z= 0.308 Angle : 0.764 11.524 60277 Z= 0.415 Chirality : 0.047 0.165 6251 Planarity : 0.009 0.170 7924 Dihedral : 6.918 55.251 5992 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 1.44 % Allowed : 8.84 % Favored : 89.72 % Rotamer: Outliers : 0.33 % Allowed : 2.65 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 3.42 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.11), residues: 5418 helix: -1.72 (0.15), residues: 847 sheet: -0.65 (0.12), residues: 1960 loop : -2.69 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 371 HIS 0.006 0.002 HIS I 186 PHE 0.019 0.002 PHE J 112 TYR 0.037 0.002 TYR I 118 ARG 0.009 0.001 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1520 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1505 time to evaluate : 4.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7244 (t0) cc_final: 0.6887 (t0) REVERT: A 127 TRP cc_start: 0.7459 (t60) cc_final: 0.6936 (t60) REVERT: A 138 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7194 (mp0) REVERT: A 182 ASP cc_start: 0.8592 (m-30) cc_final: 0.8384 (m-30) REVERT: A 331 THR cc_start: 0.4920 (p) cc_final: 0.4431 (p) REVERT: A 348 TYR cc_start: 0.9328 (t80) cc_final: 0.9071 (t80) REVERT: B 26 VAL cc_start: 0.8663 (t) cc_final: 0.8364 (t) REVERT: B 29 GLU cc_start: 0.8719 (mp0) cc_final: 0.8432 (mp0) REVERT: B 38 ILE cc_start: 0.8659 (pt) cc_final: 0.8310 (pt) REVERT: B 100 ASP cc_start: 0.9020 (m-30) cc_final: 0.8227 (t0) REVERT: B 162 TYR cc_start: 0.7929 (t80) cc_final: 0.7626 (t80) REVERT: B 331 THR cc_start: 0.5352 (p) cc_final: 0.5006 (p) REVERT: C 291 ILE cc_start: 0.9198 (mt) cc_final: 0.8985 (mp) REVERT: C 294 LYS cc_start: 0.9233 (tttt) cc_final: 0.8880 (tttt) REVERT: C 296 GLU cc_start: 0.7274 (pt0) cc_final: 0.7039 (pt0) REVERT: C 331 THR cc_start: 0.4906 (p) cc_final: 0.4439 (p) REVERT: D 41 MET cc_start: 0.8020 (mmm) cc_final: 0.7177 (tpp) REVERT: D 162 TYR cc_start: 0.8193 (t80) cc_final: 0.7916 (t80) REVERT: D 167 LYS cc_start: 0.4246 (mmtt) cc_final: 0.3428 (mmtm) REVERT: D 294 LYS cc_start: 0.9038 (tttt) cc_final: 0.8778 (tppt) REVERT: D 296 GLU cc_start: 0.7374 (pt0) cc_final: 0.6959 (pt0) REVERT: D 331 THR cc_start: 0.5361 (p) cc_final: 0.4860 (p) REVERT: D 384 THR cc_start: 0.8094 (p) cc_final: 0.7385 (p) REVERT: E 82 THR cc_start: 0.4403 (p) cc_final: 0.3907 (t) REVERT: E 127 TRP cc_start: 0.7329 (t60) cc_final: 0.6667 (t60) REVERT: E 186 HIS cc_start: 0.8213 (m170) cc_final: 0.8009 (m-70) REVERT: E 294 LYS cc_start: 0.9156 (tttt) cc_final: 0.8753 (tttt) REVERT: E 331 THR cc_start: 0.5283 (p) cc_final: 0.4780 (p) REVERT: F 29 GLU cc_start: 0.8931 (mp0) cc_final: 0.8617 (mp0) REVERT: F 38 ILE cc_start: 0.8740 (pt) cc_final: 0.8396 (pt) REVERT: F 41 MET cc_start: 0.8518 (mmm) cc_final: 0.7965 (tpp) REVERT: F 57 MET cc_start: 0.7503 (mtt) cc_final: 0.7159 (mtp) REVERT: F 65 ILE cc_start: 0.8012 (mt) cc_final: 0.7796 (mm) REVERT: F 93 ILE cc_start: 0.8156 (mm) cc_final: 0.7897 (mm) REVERT: F 127 TRP cc_start: 0.7191 (t60) cc_final: 0.6500 (t60) REVERT: F 167 LYS cc_start: 0.3911 (mmtt) cc_final: 0.3422 (mmtt) REVERT: F 294 LYS cc_start: 0.9156 (tttt) cc_final: 0.8777 (tttt) REVERT: F 296 GLU cc_start: 0.7395 (pt0) cc_final: 0.6757 (pt0) REVERT: F 331 THR cc_start: 0.5227 (p) cc_final: 0.4667 (p) REVERT: F 388 ASN cc_start: 0.9010 (m-40) cc_final: 0.8791 (t0) REVERT: F 413 ASN cc_start: 0.9253 (m-40) cc_final: 0.8734 (m-40) REVERT: G 38 ILE cc_start: 0.8823 (pt) cc_final: 0.8309 (pt) REVERT: G 57 MET cc_start: 0.7321 (mtt) cc_final: 0.7028 (mtp) REVERT: G 79 ASN cc_start: 0.7233 (m-40) cc_final: 0.6951 (m110) REVERT: G 127 TRP cc_start: 0.7842 (t60) cc_final: 0.7182 (t60) REVERT: G 167 LYS cc_start: 0.4032 (mmtt) cc_final: 0.3343 (mmtm) REVERT: G 294 LYS cc_start: 0.9047 (tttt) cc_final: 0.8782 (tttt) REVERT: G 296 GLU cc_start: 0.7688 (pt0) cc_final: 0.7339 (pt0) REVERT: G 331 THR cc_start: 0.5144 (p) cc_final: 0.4703 (p) REVERT: G 413 ASN cc_start: 0.9094 (m-40) cc_final: 0.8850 (m-40) REVERT: H 41 MET cc_start: 0.9036 (mmm) cc_final: 0.7804 (mmt) REVERT: H 167 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7739 (mtmm) REVERT: H 170 ILE cc_start: 0.8504 (mt) cc_final: 0.8245 (mt) REVERT: H 213 SER cc_start: 0.9025 (t) cc_final: 0.8616 (p) REVERT: H 393 LEU cc_start: 0.9144 (mt) cc_final: 0.8343 (tt) REVERT: I 21 ASP cc_start: 0.7570 (p0) cc_final: 0.7107 (p0) REVERT: I 41 MET cc_start: 0.8809 (mmm) cc_final: 0.8003 (mmm) REVERT: I 42 MET cc_start: 0.6811 (ptp) cc_final: 0.6463 (ptp) REVERT: I 45 TRP cc_start: 0.7566 (m100) cc_final: 0.7251 (m100) REVERT: I 170 ILE cc_start: 0.8452 (mt) cc_final: 0.8232 (mt) REVERT: I 376 THR cc_start: 0.9423 (p) cc_final: 0.9034 (p) REVERT: I 393 LEU cc_start: 0.9173 (mt) cc_final: 0.8407 (tt) REVERT: J 12 PHE cc_start: 0.7601 (m-80) cc_final: 0.7285 (m-10) REVERT: J 21 ASP cc_start: 0.7677 (p0) cc_final: 0.7321 (p0) REVERT: J 41 MET cc_start: 0.9098 (mmm) cc_final: 0.8603 (mmm) REVERT: J 45 TRP cc_start: 0.7586 (m100) cc_final: 0.7347 (m-10) REVERT: J 138 GLU cc_start: 0.7252 (tm-30) cc_final: 0.7028 (tm-30) REVERT: J 160 ASP cc_start: 0.7662 (p0) cc_final: 0.7349 (m-30) REVERT: J 195 GLN cc_start: 0.8630 (tp40) cc_final: 0.8386 (tp40) REVERT: J 344 VAL cc_start: 0.9427 (t) cc_final: 0.8591 (p) REVERT: J 393 LEU cc_start: 0.9123 (mt) cc_final: 0.8432 (tt) REVERT: J 415 GLU cc_start: 0.8361 (pt0) cc_final: 0.7624 (mt-10) REVERT: K 41 MET cc_start: 0.9164 (mmm) cc_final: 0.8775 (mmm) REVERT: K 45 TRP cc_start: 0.7222 (m100) cc_final: 0.7004 (m100) REVERT: K 170 ILE cc_start: 0.8413 (mt) cc_final: 0.8184 (mt) REVERT: K 385 MET cc_start: 0.7975 (mtm) cc_final: 0.7695 (mtt) REVERT: K 393 LEU cc_start: 0.9041 (mt) cc_final: 0.8154 (tt) REVERT: L 21 ASP cc_start: 0.7867 (p0) cc_final: 0.7401 (p0) REVERT: L 138 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7182 (tm-30) REVERT: L 213 SER cc_start: 0.8776 (t) cc_final: 0.8251 (p) REVERT: L 344 VAL cc_start: 0.9328 (t) cc_final: 0.8678 (p) REVERT: L 353 SER cc_start: 0.9563 (p) cc_final: 0.9353 (t) REVERT: L 385 MET cc_start: 0.8472 (mtm) cc_final: 0.8113 (mtt) REVERT: L 393 LEU cc_start: 0.9186 (mt) cc_final: 0.8290 (tt) REVERT: L 403 ASP cc_start: 0.8159 (p0) cc_final: 0.7904 (p0) REVERT: M 21 ASP cc_start: 0.7670 (p0) cc_final: 0.7186 (p0) REVERT: M 41 MET cc_start: 0.9109 (mmm) cc_final: 0.8834 (mmm) REVERT: M 376 THR cc_start: 0.9252 (p) cc_final: 0.9000 (p) REVERT: M 393 LEU cc_start: 0.9263 (mt) cc_final: 0.8441 (tt) REVERT: N 21 ASP cc_start: 0.7547 (p0) cc_final: 0.7052 (p0) REVERT: N 41 MET cc_start: 0.9076 (mmm) cc_final: 0.8638 (mmm) REVERT: N 138 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7270 (tm-30) REVERT: N 186 HIS cc_start: 0.8914 (t-90) cc_final: 0.8448 (t-90) REVERT: N 213 SER cc_start: 0.8688 (t) cc_final: 0.8482 (t) REVERT: N 301 ASP cc_start: 0.8449 (m-30) cc_final: 0.8178 (m-30) REVERT: N 344 VAL cc_start: 0.9293 (t) cc_final: 0.8554 (p) REVERT: N 353 SER cc_start: 0.9489 (p) cc_final: 0.9276 (t) REVERT: N 376 THR cc_start: 0.9482 (p) cc_final: 0.9262 (p) REVERT: N 382 LEU cc_start: 0.8775 (tp) cc_final: 0.8528 (tp) REVERT: N 393 LEU cc_start: 0.9199 (mt) cc_final: 0.8307 (tt) REVERT: N 409 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8733 (mm-40) outliers start: 15 outliers final: 1 residues processed: 1519 average time/residue: 1.0535 time to fit residues: 2632.1244 Evaluate side-chains 1215 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1214 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 275 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 412 optimal weight: 0.0270 chunk 337 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 496 optimal weight: 6.9990 chunk 536 optimal weight: 10.0000 chunk 442 optimal weight: 7.9990 chunk 492 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 398 optimal weight: 7.9990 overall best weight: 2.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN G 79 ASN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN H 374 ASN ** H 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN I 279 GLN J 374 ASN K 231 ASN K 279 GLN L 231 ASN ** M 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN N 380 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44142 Z= 0.274 Angle : 0.691 15.781 60277 Z= 0.367 Chirality : 0.044 0.180 6251 Planarity : 0.008 0.181 7924 Dihedral : 6.477 58.933 5992 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 1.09 % Allowed : 10.91 % Favored : 88.00 % Rotamer: Outliers : 0.09 % Allowed : 1.84 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 4.04 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 5418 helix: -1.30 (0.16), residues: 847 sheet: -0.75 (0.12), residues: 1918 loop : -2.55 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 371 HIS 0.008 0.001 HIS M 121 PHE 0.016 0.002 PHE C 12 TYR 0.021 0.002 TYR B 23 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1333 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1329 time to evaluate : 4.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASP cc_start: 0.7103 (p0) cc_final: 0.6801 (p0) REVERT: A 34 VAL cc_start: 0.8770 (t) cc_final: 0.8518 (m) REVERT: A 41 MET cc_start: 0.8342 (mmm) cc_final: 0.8130 (tpp) REVERT: A 42 MET cc_start: 0.7767 (mtp) cc_final: 0.7355 (mmt) REVERT: A 50 LEU cc_start: 0.8081 (mt) cc_final: 0.7834 (mt) REVERT: A 167 LYS cc_start: 0.3999 (mmtt) cc_final: 0.3614 (mmtm) REVERT: A 182 ASP cc_start: 0.8561 (m-30) cc_final: 0.8347 (m-30) REVERT: A 331 THR cc_start: 0.5050 (p) cc_final: 0.4710 (p) REVERT: B 100 ASP cc_start: 0.9043 (m-30) cc_final: 0.8755 (m-30) REVERT: B 331 THR cc_start: 0.5225 (p) cc_final: 0.4951 (p) REVERT: C 41 MET cc_start: 0.8357 (mmm) cc_final: 0.6963 (tpp) REVERT: C 42 MET cc_start: 0.7688 (mtp) cc_final: 0.7424 (mtp) REVERT: C 188 ASP cc_start: 0.7976 (m-30) cc_final: 0.7616 (p0) REVERT: C 294 LYS cc_start: 0.9212 (tttt) cc_final: 0.8900 (tttt) REVERT: C 331 THR cc_start: 0.4964 (p) cc_final: 0.4560 (p) REVERT: C 384 THR cc_start: 0.7993 (p) cc_final: 0.7366 (p) REVERT: D 41 MET cc_start: 0.8041 (mmm) cc_final: 0.7070 (tpp) REVERT: D 100 ASP cc_start: 0.9119 (m-30) cc_final: 0.8837 (m-30) REVERT: D 294 LYS cc_start: 0.9004 (tttt) cc_final: 0.8753 (tppt) REVERT: D 296 GLU cc_start: 0.7458 (pt0) cc_final: 0.6950 (pt0) REVERT: D 331 THR cc_start: 0.5396 (p) cc_final: 0.5040 (p) REVERT: D 384 THR cc_start: 0.8069 (p) cc_final: 0.7329 (p) REVERT: E 4 VAL cc_start: 0.8193 (p) cc_final: 0.7885 (p) REVERT: E 7 ASP cc_start: 0.7008 (p0) cc_final: 0.6764 (p0) REVERT: E 331 THR cc_start: 0.5335 (p) cc_final: 0.4998 (p) REVERT: F 7 ASP cc_start: 0.7169 (p0) cc_final: 0.6916 (p0) REVERT: F 29 GLU cc_start: 0.8950 (mp0) cc_final: 0.8629 (mp0) REVERT: F 41 MET cc_start: 0.8376 (mmm) cc_final: 0.7864 (tpp) REVERT: F 167 LYS cc_start: 0.4095 (mmtt) cc_final: 0.3747 (mmtt) REVERT: F 294 LYS cc_start: 0.9166 (tttt) cc_final: 0.8768 (tttt) REVERT: F 296 GLU cc_start: 0.7303 (pt0) cc_final: 0.6756 (pt0) REVERT: F 331 THR cc_start: 0.5147 (p) cc_final: 0.4827 (p) REVERT: F 348 TYR cc_start: 0.9174 (t80) cc_final: 0.8920 (t80) REVERT: F 413 ASN cc_start: 0.9390 (m-40) cc_final: 0.9018 (m-40) REVERT: G 7 ASP cc_start: 0.7064 (p0) cc_final: 0.6760 (p0) REVERT: G 41 MET cc_start: 0.8289 (mmm) cc_final: 0.7876 (tpp) REVERT: G 154 ASN cc_start: 0.8650 (t0) cc_final: 0.7946 (m-40) REVERT: G 167 LYS cc_start: 0.4126 (mmtt) cc_final: 0.3558 (mmtm) REVERT: G 331 THR cc_start: 0.5399 (p) cc_final: 0.5011 (p) REVERT: G 348 TYR cc_start: 0.9046 (t80) cc_final: 0.8769 (t80) REVERT: H 41 MET cc_start: 0.8927 (mmm) cc_final: 0.7841 (mmt) REVERT: H 45 TRP cc_start: 0.7824 (m100) cc_final: 0.7347 (m100) REVERT: H 185 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8524 (ttpp) REVERT: H 213 SER cc_start: 0.9049 (t) cc_final: 0.8666 (p) REVERT: H 301 ASP cc_start: 0.8301 (m-30) cc_final: 0.8026 (m-30) REVERT: H 317 THR cc_start: 0.9187 (m) cc_final: 0.8923 (p) REVERT: H 367 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7265 (tp30) REVERT: H 393 LEU cc_start: 0.9135 (mt) cc_final: 0.8528 (tt) REVERT: I 21 ASP cc_start: 0.7677 (p0) cc_final: 0.7157 (p0) REVERT: I 41 MET cc_start: 0.8695 (mmm) cc_final: 0.7848 (mmm) REVERT: I 42 MET cc_start: 0.6895 (ptp) cc_final: 0.6608 (ptp) REVERT: I 45 TRP cc_start: 0.7621 (m100) cc_final: 0.7160 (m100) REVERT: I 98 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7519 (tm-30) REVERT: I 175 PHE cc_start: 0.8089 (p90) cc_final: 0.7842 (p90) REVERT: I 195 GLN cc_start: 0.8718 (tp-100) cc_final: 0.8487 (tp-100) REVERT: I 213 SER cc_start: 0.8793 (t) cc_final: 0.8453 (p) REVERT: I 376 THR cc_start: 0.9371 (p) cc_final: 0.9085 (p) REVERT: I 393 LEU cc_start: 0.9191 (mt) cc_final: 0.8516 (tt) REVERT: I 400 ILE cc_start: 0.9489 (mm) cc_final: 0.9269 (mm) REVERT: J 12 PHE cc_start: 0.7704 (m-80) cc_final: 0.7368 (m-80) REVERT: J 21 ASP cc_start: 0.7435 (p0) cc_final: 0.7003 (p0) REVERT: J 41 MET cc_start: 0.8967 (mmm) cc_final: 0.8612 (mmm) REVERT: J 42 MET cc_start: 0.7020 (ptm) cc_final: 0.6361 (ppp) REVERT: J 56 ILE cc_start: 0.8667 (tt) cc_final: 0.8419 (tt) REVERT: J 138 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7056 (tm-30) REVERT: J 303 SER cc_start: 0.9504 (t) cc_final: 0.9291 (p) REVERT: J 393 LEU cc_start: 0.9196 (mt) cc_final: 0.8609 (tt) REVERT: K 12 PHE cc_start: 0.7679 (m-80) cc_final: 0.7250 (m-10) REVERT: K 21 ASP cc_start: 0.7701 (p0) cc_final: 0.7129 (p0) REVERT: K 41 MET cc_start: 0.9119 (mmm) cc_final: 0.8683 (mmm) REVERT: K 45 TRP cc_start: 0.7392 (m100) cc_final: 0.7103 (m100) REVERT: K 186 HIS cc_start: 0.8513 (t-90) cc_final: 0.8176 (t70) REVERT: K 195 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8786 (tp-100) REVERT: K 367 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6858 (tp30) REVERT: K 393 LEU cc_start: 0.9011 (mt) cc_final: 0.8327 (tt) REVERT: L 21 ASP cc_start: 0.7893 (p0) cc_final: 0.7435 (p0) REVERT: L 138 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6666 (tm-30) REVERT: L 139 ASP cc_start: 0.4579 (m-30) cc_final: 0.3358 (m-30) REVERT: L 213 SER cc_start: 0.8703 (t) cc_final: 0.8292 (p) REVERT: L 301 ASP cc_start: 0.7838 (m-30) cc_final: 0.7609 (m-30) REVERT: L 367 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7095 (tp30) REVERT: L 393 LEU cc_start: 0.9268 (mt) cc_final: 0.8285 (tt) REVERT: M 12 PHE cc_start: 0.7649 (m-80) cc_final: 0.7088 (m-80) REVERT: M 21 ASP cc_start: 0.7485 (p0) cc_final: 0.7089 (p0) REVERT: M 41 MET cc_start: 0.9095 (mmm) cc_final: 0.8858 (mmm) REVERT: M 367 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7135 (tp30) REVERT: M 393 LEU cc_start: 0.9234 (mt) cc_final: 0.8440 (tt) REVERT: N 21 ASP cc_start: 0.7547 (p0) cc_final: 0.7051 (p0) REVERT: N 41 MET cc_start: 0.9013 (mmm) cc_final: 0.8614 (mmm) REVERT: N 186 HIS cc_start: 0.8753 (t-90) cc_final: 0.7909 (t-170) REVERT: N 195 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8549 (tp-100) REVERT: N 213 SER cc_start: 0.8134 (t) cc_final: 0.7737 (p) REVERT: N 301 ASP cc_start: 0.8204 (m-30) cc_final: 0.8004 (m-30) REVERT: N 321 PHE cc_start: 0.8414 (p90) cc_final: 0.8097 (p90) REVERT: N 353 SER cc_start: 0.9531 (p) cc_final: 0.9309 (t) REVERT: N 393 LEU cc_start: 0.9220 (mt) cc_final: 0.8473 (tt) outliers start: 4 outliers final: 0 residues processed: 1333 average time/residue: 1.0171 time to fit residues: 2232.6619 Evaluate side-chains 1143 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1143 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 490 optimal weight: 0.9980 chunk 373 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 498 optimal weight: 4.9990 chunk 527 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 472 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 380 ASN C 380 ASN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44142 Z= 0.198 Angle : 0.618 9.061 60277 Z= 0.328 Chirality : 0.044 0.187 6251 Planarity : 0.007 0.158 7924 Dihedral : 6.031 54.100 5992 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.97 % Favored : 90.00 % Rotamer: Outliers : 0.09 % Allowed : 1.49 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 3.42 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.11), residues: 5418 helix: -0.82 (0.17), residues: 868 sheet: -0.53 (0.12), residues: 1792 loop : -2.33 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 371 HIS 0.005 0.001 HIS B 341 PHE 0.020 0.001 PHE N 12 TYR 0.014 0.001 TYR I 306 ARG 0.008 0.000 ARG E 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1293 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1289 time to evaluate : 5.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASP cc_start: 0.7210 (p0) cc_final: 0.6872 (p0) REVERT: A 42 MET cc_start: 0.7673 (mtp) cc_final: 0.7300 (mmt) REVERT: A 167 LYS cc_start: 0.3733 (mmtt) cc_final: 0.3235 (mmtm) REVERT: A 294 LYS cc_start: 0.9074 (ptmt) cc_final: 0.8702 (ptpt) REVERT: A 296 GLU cc_start: 0.7319 (pt0) cc_final: 0.6576 (pt0) REVERT: A 331 THR cc_start: 0.4715 (p) cc_final: 0.4384 (p) REVERT: B 34 VAL cc_start: 0.9002 (t) cc_final: 0.8789 (m) REVERT: B 41 MET cc_start: 0.8282 (mmm) cc_final: 0.7400 (tpp) REVERT: B 42 MET cc_start: 0.7857 (mtp) cc_final: 0.7454 (mtp) REVERT: B 100 ASP cc_start: 0.9158 (m-30) cc_final: 0.8809 (m-30) REVERT: B 167 LYS cc_start: 0.3760 (mmtt) cc_final: 0.3269 (mtpp) REVERT: C 34 VAL cc_start: 0.8688 (t) cc_final: 0.8486 (t) REVERT: C 41 MET cc_start: 0.8210 (mmm) cc_final: 0.6869 (tpp) REVERT: C 42 MET cc_start: 0.7598 (mtp) cc_final: 0.7289 (mtp) REVERT: C 182 ASP cc_start: 0.8458 (m-30) cc_final: 0.8238 (m-30) REVERT: C 188 ASP cc_start: 0.7974 (m-30) cc_final: 0.7558 (p0) REVERT: C 294 LYS cc_start: 0.9310 (tttt) cc_final: 0.8993 (tttt) REVERT: C 331 THR cc_start: 0.4591 (p) cc_final: 0.4290 (p) REVERT: D 7 ASP cc_start: 0.7323 (p0) cc_final: 0.7097 (p0) REVERT: D 29 GLU cc_start: 0.8735 (mp0) cc_final: 0.8528 (mp0) REVERT: D 41 MET cc_start: 0.7979 (mmm) cc_final: 0.7042 (tpp) REVERT: D 100 ASP cc_start: 0.9070 (m-30) cc_final: 0.8767 (m-30) REVERT: D 322 LEU cc_start: 0.7718 (tp) cc_final: 0.7503 (mp) REVERT: D 384 THR cc_start: 0.8057 (p) cc_final: 0.7324 (p) REVERT: E 7 ASP cc_start: 0.7114 (p0) cc_final: 0.6746 (p0) REVERT: E 343 PHE cc_start: 0.7329 (m-10) cc_final: 0.7121 (m-10) REVERT: F 29 GLU cc_start: 0.8626 (mp0) cc_final: 0.8312 (mp0) REVERT: F 41 MET cc_start: 0.8434 (mmm) cc_final: 0.7942 (tpp) REVERT: F 56 ILE cc_start: 0.8269 (mm) cc_final: 0.8035 (mp) REVERT: F 167 LYS cc_start: 0.4396 (mmtt) cc_final: 0.3948 (mmtm) REVERT: F 294 LYS cc_start: 0.9150 (tttt) cc_final: 0.8742 (tttt) REVERT: F 296 GLU cc_start: 0.7225 (pt0) cc_final: 0.6805 (pt0) REVERT: F 331 THR cc_start: 0.5077 (p) cc_final: 0.4841 (p) REVERT: F 348 TYR cc_start: 0.9156 (t80) cc_final: 0.8851 (t80) REVERT: F 413 ASN cc_start: 0.9359 (m-40) cc_final: 0.8972 (m-40) REVERT: G 7 ASP cc_start: 0.7253 (p0) cc_final: 0.6933 (p0) REVERT: G 41 MET cc_start: 0.8333 (mmm) cc_final: 0.8038 (tpp) REVERT: G 154 ASN cc_start: 0.8622 (t0) cc_final: 0.8386 (m-40) REVERT: G 167 LYS cc_start: 0.3637 (mmtt) cc_final: 0.3426 (mmtm) REVERT: G 331 THR cc_start: 0.5171 (p) cc_final: 0.4812 (p) REVERT: G 348 TYR cc_start: 0.8999 (t80) cc_final: 0.8793 (t80) REVERT: H 41 MET cc_start: 0.8932 (mmm) cc_final: 0.7880 (mmt) REVERT: H 45 TRP cc_start: 0.7742 (m100) cc_final: 0.7237 (m100) REVERT: H 170 ILE cc_start: 0.8350 (mt) cc_final: 0.8137 (mt) REVERT: H 213 SER cc_start: 0.9008 (t) cc_final: 0.8615 (p) REVERT: H 301 ASP cc_start: 0.8177 (m-30) cc_final: 0.7934 (m-30) REVERT: H 393 LEU cc_start: 0.9192 (mt) cc_final: 0.8327 (tt) REVERT: I 21 ASP cc_start: 0.7596 (p0) cc_final: 0.7085 (p0) REVERT: I 27 ASN cc_start: 0.7239 (p0) cc_final: 0.6667 (p0) REVERT: I 41 MET cc_start: 0.8661 (mmm) cc_final: 0.7877 (mmm) REVERT: I 42 MET cc_start: 0.6809 (ptp) cc_final: 0.6559 (ptp) REVERT: I 45 TRP cc_start: 0.7695 (m100) cc_final: 0.7415 (m100) REVERT: I 98 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7439 (tm-30) REVERT: I 175 PHE cc_start: 0.8147 (p90) cc_final: 0.7770 (p90) REVERT: I 195 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8406 (tp-100) REVERT: I 376 THR cc_start: 0.9235 (p) cc_final: 0.8948 (p) REVERT: I 393 LEU cc_start: 0.9357 (mt) cc_final: 0.8601 (tt) REVERT: J 12 PHE cc_start: 0.7862 (m-80) cc_final: 0.7487 (m-80) REVERT: J 21 ASP cc_start: 0.7491 (p0) cc_final: 0.7147 (p0) REVERT: J 41 MET cc_start: 0.9034 (mmm) cc_final: 0.8683 (mmm) REVERT: J 138 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7029 (tm-30) REVERT: J 186 HIS cc_start: 0.8770 (t70) cc_final: 0.8269 (t70) REVERT: J 393 LEU cc_start: 0.9301 (mt) cc_final: 0.8537 (tt) REVERT: K 12 PHE cc_start: 0.7751 (m-80) cc_final: 0.7231 (m-80) REVERT: K 21 ASP cc_start: 0.7650 (p0) cc_final: 0.6985 (p0) REVERT: K 41 MET cc_start: 0.9196 (mmm) cc_final: 0.8680 (mmm) REVERT: K 45 TRP cc_start: 0.7482 (m100) cc_final: 0.7112 (m100) REVERT: K 186 HIS cc_start: 0.8615 (t-90) cc_final: 0.8061 (t70) REVERT: K 195 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8639 (tp-100) REVERT: K 367 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7197 (tp30) REVERT: K 393 LEU cc_start: 0.9168 (mt) cc_final: 0.8256 (tt) REVERT: L 42 MET cc_start: 0.6741 (ptm) cc_final: 0.5525 (ppp) REVERT: L 186 HIS cc_start: 0.8738 (t70) cc_final: 0.8044 (t-170) REVERT: L 195 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8448 (tp-100) REVERT: L 213 SER cc_start: 0.8592 (t) cc_final: 0.8202 (p) REVERT: L 301 ASP cc_start: 0.7835 (m-30) cc_final: 0.7589 (m-30) REVERT: L 367 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6921 (tp30) REVERT: L 393 LEU cc_start: 0.9234 (mt) cc_final: 0.8491 (tt) REVERT: M 12 PHE cc_start: 0.7658 (m-80) cc_final: 0.7006 (m-80) REVERT: M 21 ASP cc_start: 0.7494 (p0) cc_final: 0.7159 (p0) REVERT: M 41 MET cc_start: 0.9049 (mmm) cc_final: 0.8453 (mmm) REVERT: M 393 LEU cc_start: 0.9231 (mt) cc_final: 0.8588 (tt) REVERT: N 21 ASP cc_start: 0.7448 (p0) cc_final: 0.6940 (p0) REVERT: N 41 MET cc_start: 0.8985 (mmm) cc_final: 0.8573 (mmm) REVERT: N 213 SER cc_start: 0.8100 (t) cc_final: 0.7702 (p) REVERT: N 353 SER cc_start: 0.9541 (p) cc_final: 0.9228 (t) REVERT: N 393 LEU cc_start: 0.9306 (mt) cc_final: 0.8459 (tt) outliers start: 4 outliers final: 0 residues processed: 1293 average time/residue: 1.0310 time to fit residues: 2210.6125 Evaluate side-chains 1101 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1101 time to evaluate : 4.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 439 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 450 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 473 optimal weight: 10.0000 chunk 133 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: D 341 HIS E 341 HIS F 341 HIS ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 ASN J 102 GLN J 186 HIS ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 ASN ** M 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN N 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 44142 Z= 0.315 Angle : 0.683 16.432 60277 Z= 0.359 Chirality : 0.044 0.161 6251 Planarity : 0.008 0.182 7924 Dihedral : 6.109 51.677 5992 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 1.14 % Allowed : 11.52 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 2.48 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 5418 helix: -0.77 (0.17), residues: 868 sheet: -0.88 (0.12), residues: 1897 loop : -2.38 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 371 HIS 0.006 0.001 HIS H 121 PHE 0.014 0.002 PHE F 12 TYR 0.024 0.002 TYR M 118 ARG 0.011 0.001 ARG N 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1183 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1183 time to evaluate : 4.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASP cc_start: 0.7479 (p0) cc_final: 0.7038 (p0) REVERT: A 167 LYS cc_start: 0.3569 (mmtt) cc_final: 0.2826 (mmtt) REVERT: A 296 GLU cc_start: 0.7352 (pt0) cc_final: 0.6778 (pt0) REVERT: A 321 PHE cc_start: 0.8961 (p90) cc_final: 0.8756 (p90) REVERT: A 331 THR cc_start: 0.5027 (p) cc_final: 0.4671 (p) REVERT: B 41 MET cc_start: 0.8224 (mmm) cc_final: 0.7475 (tpp) REVERT: B 42 MET cc_start: 0.8034 (mtp) cc_final: 0.7787 (mtp) REVERT: B 100 ASP cc_start: 0.9101 (m-30) cc_final: 0.8709 (m-30) REVERT: B 162 TYR cc_start: 0.7709 (t80) cc_final: 0.7506 (t80) REVERT: B 167 LYS cc_start: 0.4029 (mmtt) cc_final: 0.3488 (mtpp) REVERT: B 296 GLU cc_start: 0.7336 (pt0) cc_final: 0.7135 (pt0) REVERT: B 331 THR cc_start: 0.4924 (p) cc_final: 0.4619 (p) REVERT: C 41 MET cc_start: 0.8212 (mmm) cc_final: 0.6856 (tpp) REVERT: C 42 MET cc_start: 0.7691 (mtp) cc_final: 0.7417 (mtp) REVERT: C 167 LYS cc_start: 0.3975 (mmtt) cc_final: 0.3523 (mmtt) REVERT: C 188 ASP cc_start: 0.8032 (m-30) cc_final: 0.7579 (p0) REVERT: C 294 LYS cc_start: 0.9348 (tttt) cc_final: 0.9011 (tttt) REVERT: C 331 THR cc_start: 0.4952 (p) cc_final: 0.4645 (p) REVERT: C 384 THR cc_start: 0.7867 (p) cc_final: 0.7043 (p) REVERT: D 7 ASP cc_start: 0.7384 (p0) cc_final: 0.7031 (p0) REVERT: D 41 MET cc_start: 0.7946 (mmm) cc_final: 0.7059 (tpp) REVERT: D 50 LEU cc_start: 0.8623 (mt) cc_final: 0.8144 (mp) REVERT: D 100 ASP cc_start: 0.9286 (m-30) cc_final: 0.9042 (m-30) REVERT: D 167 LYS cc_start: 0.3779 (mmtt) cc_final: 0.3033 (mtpp) REVERT: D 296 GLU cc_start: 0.7280 (pt0) cc_final: 0.6958 (pt0) REVERT: D 331 THR cc_start: 0.5290 (p) cc_final: 0.4942 (p) REVERT: D 384 THR cc_start: 0.8057 (p) cc_final: 0.7344 (p) REVERT: E 7 ASP cc_start: 0.7270 (p0) cc_final: 0.6875 (p0) REVERT: E 50 LEU cc_start: 0.8537 (mt) cc_final: 0.8032 (mp) REVERT: E 167 LYS cc_start: 0.4000 (mmtt) cc_final: 0.3630 (mmtt) REVERT: F 41 MET cc_start: 0.8486 (mmm) cc_final: 0.7887 (tpp) REVERT: F 167 LYS cc_start: 0.4437 (mmtt) cc_final: 0.4141 (mmtm) REVERT: F 294 LYS cc_start: 0.9140 (tttt) cc_final: 0.8772 (tttt) REVERT: F 296 GLU cc_start: 0.7367 (pt0) cc_final: 0.6860 (pt0) REVERT: F 331 THR cc_start: 0.5330 (p) cc_final: 0.4971 (p) REVERT: F 348 TYR cc_start: 0.9124 (t80) cc_final: 0.8920 (t80) REVERT: F 413 ASN cc_start: 0.9382 (m-40) cc_final: 0.8895 (m-40) REVERT: G 7 ASP cc_start: 0.7239 (p0) cc_final: 0.7000 (p0) REVERT: G 41 MET cc_start: 0.8370 (mmm) cc_final: 0.7941 (tpp) REVERT: G 154 ASN cc_start: 0.8765 (t0) cc_final: 0.8527 (m-40) REVERT: G 331 THR cc_start: 0.5404 (p) cc_final: 0.5149 (p) REVERT: G 348 TYR cc_start: 0.9059 (t80) cc_final: 0.8825 (t80) REVERT: H 41 MET cc_start: 0.8852 (mmm) cc_final: 0.7923 (mmt) REVERT: H 45 TRP cc_start: 0.7913 (m100) cc_final: 0.7179 (m100) REVERT: H 98 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7933 (tm-30) REVERT: H 167 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7813 (mtmm) REVERT: H 175 PHE cc_start: 0.8595 (p90) cc_final: 0.8228 (p90) REVERT: H 186 HIS cc_start: 0.8763 (t70) cc_final: 0.8280 (t70) REVERT: H 213 SER cc_start: 0.8663 (t) cc_final: 0.8342 (p) REVERT: H 393 LEU cc_start: 0.9228 (mt) cc_final: 0.8351 (tt) REVERT: I 21 ASP cc_start: 0.7735 (p0) cc_final: 0.7127 (p0) REVERT: I 41 MET cc_start: 0.8705 (mmm) cc_final: 0.7960 (mmm) REVERT: I 42 MET cc_start: 0.7075 (ptp) cc_final: 0.6870 (ptp) REVERT: I 45 TRP cc_start: 0.7856 (m100) cc_final: 0.7524 (m100) REVERT: I 98 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7562 (tm-30) REVERT: I 175 PHE cc_start: 0.8472 (p90) cc_final: 0.8045 (p90) REVERT: I 195 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8452 (tp-100) REVERT: I 213 SER cc_start: 0.8825 (t) cc_final: 0.8588 (p) REVERT: I 353 SER cc_start: 0.9631 (p) cc_final: 0.9429 (t) REVERT: I 393 LEU cc_start: 0.9374 (mt) cc_final: 0.8585 (tt) REVERT: J 12 PHE cc_start: 0.7775 (m-80) cc_final: 0.7563 (m-80) REVERT: J 21 ASP cc_start: 0.7197 (p0) cc_final: 0.6674 (p0) REVERT: J 41 MET cc_start: 0.8989 (mmm) cc_final: 0.8607 (mmm) REVERT: J 42 MET cc_start: 0.6992 (ptp) cc_final: 0.6780 (ptp) REVERT: J 138 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7373 (tm-30) REVERT: J 145 ASP cc_start: 0.7818 (t70) cc_final: 0.7587 (m-30) REVERT: J 175 PHE cc_start: 0.8459 (p90) cc_final: 0.8199 (p90) REVERT: J 186 HIS cc_start: 0.8600 (t-90) cc_final: 0.8297 (t70) REVERT: J 393 LEU cc_start: 0.9310 (mt) cc_final: 0.8493 (tt) REVERT: K 12 PHE cc_start: 0.7808 (m-80) cc_final: 0.7100 (m-80) REVERT: K 21 ASP cc_start: 0.7699 (p0) cc_final: 0.7106 (p0) REVERT: K 41 MET cc_start: 0.9233 (mmm) cc_final: 0.8572 (mmm) REVERT: K 45 TRP cc_start: 0.7941 (m100) cc_final: 0.7468 (m100) REVERT: K 66 LYS cc_start: 0.6401 (mmtt) cc_final: 0.6110 (mmtt) REVERT: K 186 HIS cc_start: 0.8548 (t-90) cc_final: 0.8170 (t70) REVERT: K 388 ASN cc_start: 0.7016 (t0) cc_final: 0.6746 (t0) REVERT: K 393 LEU cc_start: 0.9248 (mt) cc_final: 0.8261 (tt) REVERT: K 401 THR cc_start: 0.8256 (p) cc_final: 0.8055 (p) REVERT: L 21 ASP cc_start: 0.8275 (p0) cc_final: 0.7838 (p0) REVERT: L 41 MET cc_start: 0.8669 (mmm) cc_final: 0.8274 (mmm) REVERT: L 42 MET cc_start: 0.6327 (ptm) cc_final: 0.5202 (ppp) REVERT: L 98 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7480 (tm-30) REVERT: L 145 ASP cc_start: 0.7708 (t70) cc_final: 0.7150 (m-30) REVERT: L 175 PHE cc_start: 0.8459 (p90) cc_final: 0.8099 (p90) REVERT: L 186 HIS cc_start: 0.8690 (t70) cc_final: 0.6906 (t-170) REVERT: L 195 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8320 (tp-100) REVERT: L 207 ASP cc_start: 0.8306 (m-30) cc_final: 0.8102 (m-30) REVERT: L 301 ASP cc_start: 0.8159 (m-30) cc_final: 0.7849 (m-30) REVERT: L 344 VAL cc_start: 0.9198 (t) cc_final: 0.8944 (t) REVERT: L 393 LEU cc_start: 0.9367 (mt) cc_final: 0.8474 (tt) REVERT: M 12 PHE cc_start: 0.7744 (m-80) cc_final: 0.6903 (m-80) REVERT: M 21 ASP cc_start: 0.7354 (p0) cc_final: 0.6985 (p0) REVERT: M 41 MET cc_start: 0.9068 (mmm) cc_final: 0.8499 (mmm) REVERT: M 45 TRP cc_start: 0.7992 (m100) cc_final: 0.7754 (m100) REVERT: M 175 PHE cc_start: 0.8524 (p90) cc_final: 0.8294 (p90) REVERT: M 358 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8449 (mm-40) REVERT: M 393 LEU cc_start: 0.9306 (mt) cc_final: 0.8690 (tt) REVERT: N 21 ASP cc_start: 0.7436 (p0) cc_final: 0.6829 (p0) REVERT: N 41 MET cc_start: 0.8983 (mmm) cc_final: 0.8411 (mmm) REVERT: N 42 MET cc_start: 0.7522 (ptp) cc_final: 0.7182 (pmm) REVERT: N 45 TRP cc_start: 0.8054 (m100) cc_final: 0.7677 (m100) REVERT: N 186 HIS cc_start: 0.8623 (t-170) cc_final: 0.8075 (t-170) REVERT: N 207 ASP cc_start: 0.8397 (m-30) cc_final: 0.8184 (m-30) REVERT: N 213 SER cc_start: 0.8440 (t) cc_final: 0.8129 (p) REVERT: N 339 TRP cc_start: 0.8715 (t-100) cc_final: 0.8459 (t-100) REVERT: N 344 VAL cc_start: 0.9343 (t) cc_final: 0.8558 (t) REVERT: N 353 SER cc_start: 0.9563 (p) cc_final: 0.9276 (t) REVERT: N 367 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7345 (tp30) REVERT: N 393 LEU cc_start: 0.9185 (mt) cc_final: 0.8418 (tt) outliers start: 0 outliers final: 0 residues processed: 1183 average time/residue: 1.0303 time to fit residues: 2016.8920 Evaluate side-chains 1049 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1049 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 177 optimal weight: 0.8980 chunk 475 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 528 optimal weight: 0.8980 chunk 438 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN G 132 HIS H 107 HIS ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 ASN M 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 44142 Z= 0.184 Angle : 0.595 7.692 60277 Z= 0.314 Chirality : 0.043 0.182 6251 Planarity : 0.007 0.148 7924 Dihedral : 5.765 49.813 5992 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.90 % Favored : 90.09 % Rotamer: Outliers : 0.18 % Allowed : 0.66 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 2.17 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 5418 helix: -0.58 (0.17), residues: 910 sheet: -0.75 (0.12), residues: 1855 loop : -2.17 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 371 HIS 0.006 0.001 HIS M 121 PHE 0.015 0.001 PHE N 321 TYR 0.017 0.001 TYR I 306 ARG 0.007 0.000 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1150 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1142 time to evaluate : 4.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASP cc_start: 0.7395 (p0) cc_final: 0.7043 (p0) REVERT: A 167 LYS cc_start: 0.3349 (mmtt) cc_final: 0.2491 (mmtm) REVERT: A 186 HIS cc_start: 0.8488 (m-70) cc_final: 0.8166 (m-70) REVERT: A 296 GLU cc_start: 0.7338 (pt0) cc_final: 0.6865 (pt0) REVERT: A 321 PHE cc_start: 0.8890 (p90) cc_final: 0.8620 (p90) REVERT: B 41 MET cc_start: 0.8167 (mmm) cc_final: 0.7432 (tpp) REVERT: B 100 ASP cc_start: 0.9110 (m-30) cc_final: 0.8761 (m-30) REVERT: B 162 TYR cc_start: 0.7540 (t80) cc_final: 0.7325 (t80) REVERT: B 167 LYS cc_start: 0.3660 (mmtt) cc_final: 0.3172 (mtpp) REVERT: B 384 THR cc_start: 0.7819 (m) cc_final: 0.7510 (m) REVERT: C 29 GLU cc_start: 0.8627 (mp0) cc_final: 0.8409 (mm-30) REVERT: C 41 MET cc_start: 0.7919 (mmm) cc_final: 0.6822 (tpp) REVERT: C 167 LYS cc_start: 0.3938 (mmtt) cc_final: 0.3455 (mmtt) REVERT: C 182 ASP cc_start: 0.8529 (m-30) cc_final: 0.8316 (m-30) REVERT: C 294 LYS cc_start: 0.9329 (tttt) cc_final: 0.9026 (tttt) REVERT: D 41 MET cc_start: 0.7807 (mmm) cc_final: 0.6969 (tpp) REVERT: D 50 LEU cc_start: 0.8845 (mt) cc_final: 0.8410 (mp) REVERT: D 57 MET cc_start: 0.7435 (mtp) cc_final: 0.7120 (mtp) REVERT: D 100 ASP cc_start: 0.9065 (m-30) cc_final: 0.8615 (m-30) REVERT: D 167 LYS cc_start: 0.3617 (mmtt) cc_final: 0.3002 (mttm) REVERT: D 296 GLU cc_start: 0.7203 (pt0) cc_final: 0.6897 (pt0) REVERT: D 384 THR cc_start: 0.7994 (p) cc_final: 0.7290 (p) REVERT: E 50 LEU cc_start: 0.8571 (mt) cc_final: 0.8011 (mp) REVERT: E 57 MET cc_start: 0.6925 (mtp) cc_final: 0.6669 (mtp) REVERT: E 93 ILE cc_start: 0.8310 (mm) cc_final: 0.8071 (mm) REVERT: E 167 LYS cc_start: 0.3764 (mmtt) cc_final: 0.3420 (mttt) REVERT: E 180 ASP cc_start: 0.8402 (m-30) cc_final: 0.8191 (m-30) REVERT: E 296 GLU cc_start: 0.7367 (pt0) cc_final: 0.6982 (pt0) REVERT: F 29 GLU cc_start: 0.8622 (mp0) cc_final: 0.8382 (mm-30) REVERT: F 41 MET cc_start: 0.8383 (mmm) cc_final: 0.7877 (tpp) REVERT: F 167 LYS cc_start: 0.4461 (mmtt) cc_final: 0.3840 (mmtm) REVERT: F 294 LYS cc_start: 0.9109 (tttt) cc_final: 0.8855 (tttt) REVERT: F 296 GLU cc_start: 0.7319 (pt0) cc_final: 0.6897 (pt0) REVERT: F 331 THR cc_start: 0.4888 (p) cc_final: 0.4654 (p) REVERT: F 348 TYR cc_start: 0.9148 (t80) cc_final: 0.8914 (t80) REVERT: F 413 ASN cc_start: 0.9431 (m-40) cc_final: 0.9000 (m-40) REVERT: G 7 ASP cc_start: 0.7246 (p0) cc_final: 0.6954 (p0) REVERT: G 41 MET cc_start: 0.8314 (mmm) cc_final: 0.7930 (tpp) REVERT: G 42 MET cc_start: 0.7815 (mtp) cc_final: 0.7442 (mtp) REVERT: G 155 ASN cc_start: 0.8755 (t0) cc_final: 0.8493 (t0) REVERT: G 321 PHE cc_start: 0.8988 (p90) cc_final: 0.8713 (p90) REVERT: G 322 LEU cc_start: 0.8245 (tp) cc_final: 0.7944 (mp) REVERT: H 41 MET cc_start: 0.8846 (mmm) cc_final: 0.7963 (mmt) REVERT: H 98 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7667 (tm-30) REVERT: H 167 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7804 (mtmm) REVERT: H 175 PHE cc_start: 0.8475 (p90) cc_final: 0.7990 (p90) REVERT: H 186 HIS cc_start: 0.8612 (t70) cc_final: 0.8080 (t-170) REVERT: H 213 SER cc_start: 0.8685 (t) cc_final: 0.8464 (p) REVERT: H 367 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7465 (tp30) REVERT: H 393 LEU cc_start: 0.9184 (mt) cc_final: 0.8405 (tt) REVERT: I 12 PHE cc_start: 0.7709 (m-80) cc_final: 0.6691 (m-80) REVERT: I 21 ASP cc_start: 0.7694 (p0) cc_final: 0.7120 (p0) REVERT: I 41 MET cc_start: 0.8679 (mmm) cc_final: 0.7953 (mmm) REVERT: I 42 MET cc_start: 0.6971 (ptp) cc_final: 0.6674 (ptp) REVERT: I 98 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7490 (tm-30) REVERT: I 175 PHE cc_start: 0.8466 (p90) cc_final: 0.7985 (p90) REVERT: I 186 HIS cc_start: 0.8650 (t-90) cc_final: 0.8247 (t70) REVERT: I 195 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8324 (tp-100) REVERT: I 213 SER cc_start: 0.8896 (t) cc_final: 0.8558 (p) REVERT: I 393 LEU cc_start: 0.9384 (mt) cc_final: 0.8594 (tt) REVERT: J 21 ASP cc_start: 0.7358 (p0) cc_final: 0.6993 (p0) REVERT: J 41 MET cc_start: 0.8954 (mmm) cc_final: 0.8577 (mmm) REVERT: J 175 PHE cc_start: 0.8308 (p90) cc_final: 0.8009 (p90) REVERT: J 186 HIS cc_start: 0.8612 (t-90) cc_final: 0.8237 (t70) REVERT: J 393 LEU cc_start: 0.9249 (mt) cc_final: 0.8563 (tt) REVERT: K 12 PHE cc_start: 0.7848 (m-80) cc_final: 0.7248 (m-80) REVERT: K 41 MET cc_start: 0.9139 (mmm) cc_final: 0.8502 (mmm) REVERT: K 186 HIS cc_start: 0.8528 (t-90) cc_final: 0.8228 (t70) REVERT: K 213 SER cc_start: 0.8629 (m) cc_final: 0.8209 (p) REVERT: K 367 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7269 (tp30) REVERT: K 393 LEU cc_start: 0.9209 (mt) cc_final: 0.8372 (tt) REVERT: L 21 ASP cc_start: 0.8196 (p0) cc_final: 0.7669 (p0) REVERT: L 41 MET cc_start: 0.8676 (mmm) cc_final: 0.8288 (mmm) REVERT: L 42 MET cc_start: 0.6143 (ptm) cc_final: 0.5087 (ppp) REVERT: L 98 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7372 (tm-30) REVERT: L 145 ASP cc_start: 0.7673 (t70) cc_final: 0.7323 (m-30) REVERT: L 175 PHE cc_start: 0.8361 (p90) cc_final: 0.7940 (p90) REVERT: L 179 LEU cc_start: 0.8631 (tt) cc_final: 0.8317 (tt) REVERT: L 207 ASP cc_start: 0.8300 (m-30) cc_final: 0.8030 (m-30) REVERT: L 301 ASP cc_start: 0.7715 (m-30) cc_final: 0.7509 (m-30) REVERT: L 344 VAL cc_start: 0.9210 (t) cc_final: 0.8910 (t) REVERT: L 367 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6966 (tp30) REVERT: L 376 THR cc_start: 0.9078 (p) cc_final: 0.8874 (p) REVERT: L 393 LEU cc_start: 0.9321 (mt) cc_final: 0.8508 (tt) REVERT: M 12 PHE cc_start: 0.7747 (m-80) cc_final: 0.6932 (m-80) REVERT: M 21 ASP cc_start: 0.7430 (p0) cc_final: 0.7081 (p0) REVERT: M 41 MET cc_start: 0.8962 (mmm) cc_final: 0.8310 (mmm) REVERT: M 166 ASP cc_start: 0.7602 (t0) cc_final: 0.7351 (t0) REVERT: M 195 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8568 (tp-100) REVERT: M 212 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7827 (mm-40) REVERT: M 321 PHE cc_start: 0.8498 (p90) cc_final: 0.7896 (p90) REVERT: M 393 LEU cc_start: 0.9338 (mt) cc_final: 0.8754 (tt) REVERT: N 21 ASP cc_start: 0.7481 (p0) cc_final: 0.6897 (p0) REVERT: N 41 MET cc_start: 0.9034 (mmm) cc_final: 0.8619 (mmm) REVERT: N 213 SER cc_start: 0.8574 (t) cc_final: 0.8197 (p) REVERT: N 339 TRP cc_start: 0.8631 (t-100) cc_final: 0.8374 (t-100) REVERT: N 344 VAL cc_start: 0.9309 (t) cc_final: 0.8541 (t) REVERT: N 353 SER cc_start: 0.9603 (p) cc_final: 0.9289 (t) REVERT: N 367 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7063 (tp30) REVERT: N 393 LEU cc_start: 0.9343 (mt) cc_final: 0.8501 (tt) outliers start: 8 outliers final: 7 residues processed: 1150 average time/residue: 0.9966 time to fit residues: 1922.2825 Evaluate side-chains 1029 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1022 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 509 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 385 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 444 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 526 optimal weight: 0.7980 chunk 329 optimal weight: 7.9990 chunk 320 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 340 ASN ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 ASN L 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44142 Z= 0.177 Angle : 0.586 15.045 60277 Z= 0.303 Chirality : 0.043 0.176 6251 Planarity : 0.007 0.172 7924 Dihedral : 5.533 48.238 5992 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.11 % Favored : 88.96 % Rotamer: Outliers : 0.02 % Allowed : 0.53 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 2.17 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.11), residues: 5418 helix: -0.28 (0.17), residues: 903 sheet: -0.51 (0.12), residues: 1834 loop : -2.15 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 371 HIS 0.012 0.001 HIS N 186 PHE 0.015 0.001 PHE A 308 TYR 0.015 0.001 TYR M 348 ARG 0.007 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1105 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1104 time to evaluate : 5.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASP cc_start: 0.7345 (p0) cc_final: 0.6985 (p0) REVERT: A 167 LYS cc_start: 0.3350 (mmtt) cc_final: 0.2677 (mmtm) REVERT: A 186 HIS cc_start: 0.8522 (m-70) cc_final: 0.8211 (m-70) REVERT: A 296 GLU cc_start: 0.7315 (pt0) cc_final: 0.6794 (pt0) REVERT: A 321 PHE cc_start: 0.8875 (p90) cc_final: 0.8595 (p90) REVERT: A 404 PHE cc_start: 0.5523 (t80) cc_final: 0.5087 (t80) REVERT: B 41 MET cc_start: 0.7903 (mmm) cc_final: 0.7350 (tpp) REVERT: B 100 ASP cc_start: 0.9102 (m-30) cc_final: 0.8768 (m-30) REVERT: B 167 LYS cc_start: 0.3784 (mmtt) cc_final: 0.3261 (mtpp) REVERT: B 209 ASP cc_start: 0.6835 (m-30) cc_final: 0.6589 (m-30) REVERT: B 296 GLU cc_start: 0.7324 (pt0) cc_final: 0.7073 (pt0) REVERT: B 413 ASN cc_start: 0.9034 (m-40) cc_final: 0.8667 (m-40) REVERT: C 41 MET cc_start: 0.8068 (mmm) cc_final: 0.7015 (tpp) REVERT: C 167 LYS cc_start: 0.3916 (mmtt) cc_final: 0.3334 (mmtt) REVERT: C 294 LYS cc_start: 0.9242 (tttt) cc_final: 0.8967 (tttt) REVERT: C 384 THR cc_start: 0.7714 (p) cc_final: 0.6903 (p) REVERT: D 41 MET cc_start: 0.7766 (mmm) cc_final: 0.6922 (tpp) REVERT: D 50 LEU cc_start: 0.8852 (mt) cc_final: 0.8420 (mp) REVERT: D 57 MET cc_start: 0.7313 (mtp) cc_final: 0.7077 (mtp) REVERT: D 100 ASP cc_start: 0.9069 (m-30) cc_final: 0.8626 (m-30) REVERT: D 167 LYS cc_start: 0.3371 (mmtt) cc_final: 0.2679 (mttm) REVERT: D 296 GLU cc_start: 0.7253 (pt0) cc_final: 0.6902 (pt0) REVERT: D 384 THR cc_start: 0.7926 (p) cc_final: 0.7307 (p) REVERT: E 50 LEU cc_start: 0.8669 (mt) cc_final: 0.8167 (mp) REVERT: E 57 MET cc_start: 0.6786 (mtp) cc_final: 0.6505 (mtp) REVERT: E 93 ILE cc_start: 0.8303 (mm) cc_final: 0.8035 (mm) REVERT: E 167 LYS cc_start: 0.3368 (mmtt) cc_final: 0.2998 (mttt) REVERT: E 180 ASP cc_start: 0.8310 (m-30) cc_final: 0.8056 (m-30) REVERT: E 296 GLU cc_start: 0.7284 (pt0) cc_final: 0.6977 (pt0) REVERT: E 321 PHE cc_start: 0.8650 (p90) cc_final: 0.8429 (p90) REVERT: F 29 GLU cc_start: 0.8621 (mp0) cc_final: 0.8205 (mm-30) REVERT: F 41 MET cc_start: 0.8404 (mmm) cc_final: 0.7807 (tpp) REVERT: F 42 MET cc_start: 0.8022 (mtp) cc_final: 0.7599 (mtp) REVERT: F 167 LYS cc_start: 0.4365 (mmtt) cc_final: 0.3753 (mmtm) REVERT: F 294 LYS cc_start: 0.9095 (tttt) cc_final: 0.8878 (tttt) REVERT: F 296 GLU cc_start: 0.7333 (pt0) cc_final: 0.6879 (pt0) REVERT: F 348 TYR cc_start: 0.9161 (t80) cc_final: 0.8897 (t80) REVERT: F 413 ASN cc_start: 0.9419 (m-40) cc_final: 0.8975 (m-40) REVERT: G 41 MET cc_start: 0.8336 (mmm) cc_final: 0.7811 (tpp) REVERT: G 42 MET cc_start: 0.7100 (mtp) cc_final: 0.6706 (mtp) REVERT: G 155 ASN cc_start: 0.8730 (t0) cc_final: 0.8421 (t0) REVERT: G 321 PHE cc_start: 0.9025 (p90) cc_final: 0.8731 (p90) REVERT: G 322 LEU cc_start: 0.8312 (tp) cc_final: 0.8003 (mp) REVERT: G 413 ASN cc_start: 0.9048 (m-40) cc_final: 0.8731 (m-40) REVERT: H 12 PHE cc_start: 0.7536 (m-80) cc_final: 0.6944 (m-80) REVERT: H 41 MET cc_start: 0.8850 (mmm) cc_final: 0.8029 (mmt) REVERT: H 98 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7522 (tm-30) REVERT: H 167 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7855 (mtmm) REVERT: H 175 PHE cc_start: 0.8498 (p90) cc_final: 0.8070 (p90) REVERT: H 186 HIS cc_start: 0.8628 (t70) cc_final: 0.8070 (t-170) REVERT: H 213 SER cc_start: 0.8793 (t) cc_final: 0.8478 (p) REVERT: H 367 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7430 (tp30) REVERT: H 393 LEU cc_start: 0.9197 (mt) cc_final: 0.8436 (tt) REVERT: I 12 PHE cc_start: 0.7670 (m-80) cc_final: 0.6886 (m-80) REVERT: I 21 ASP cc_start: 0.7851 (p0) cc_final: 0.7311 (p0) REVERT: I 41 MET cc_start: 0.8671 (mmm) cc_final: 0.7991 (mtt) REVERT: I 42 MET cc_start: 0.6950 (ptp) cc_final: 0.6644 (ptp) REVERT: I 62 ASN cc_start: 0.7548 (t0) cc_final: 0.7343 (t0) REVERT: I 98 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7526 (tm-30) REVERT: I 175 PHE cc_start: 0.8474 (p90) cc_final: 0.7911 (p90) REVERT: I 186 HIS cc_start: 0.8642 (t-90) cc_final: 0.8257 (t70) REVERT: I 195 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8365 (tp-100) REVERT: I 213 SER cc_start: 0.8704 (t) cc_final: 0.8335 (p) REVERT: I 393 LEU cc_start: 0.9421 (mt) cc_final: 0.8687 (tt) REVERT: J 21 ASP cc_start: 0.7495 (p0) cc_final: 0.7151 (p0) REVERT: J 41 MET cc_start: 0.8939 (mmm) cc_final: 0.8642 (mmm) REVERT: J 175 PHE cc_start: 0.8364 (p90) cc_final: 0.8039 (p90) REVERT: J 186 HIS cc_start: 0.8590 (t-90) cc_final: 0.8248 (t70) REVERT: J 393 LEU cc_start: 0.9253 (mt) cc_final: 0.8686 (tt) REVERT: K 12 PHE cc_start: 0.7798 (m-80) cc_final: 0.7178 (m-80) REVERT: K 21 ASP cc_start: 0.7621 (p0) cc_final: 0.6992 (p0) REVERT: K 41 MET cc_start: 0.9092 (mmm) cc_final: 0.8606 (mmm) REVERT: K 95 ASP cc_start: 0.8771 (t0) cc_final: 0.8552 (t0) REVERT: K 186 HIS cc_start: 0.8650 (t-90) cc_final: 0.8228 (t70) REVERT: K 367 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7130 (tp30) REVERT: K 393 LEU cc_start: 0.9196 (mt) cc_final: 0.8255 (tt) REVERT: L 21 ASP cc_start: 0.8191 (p0) cc_final: 0.7651 (p0) REVERT: L 41 MET cc_start: 0.8671 (mmm) cc_final: 0.8310 (mmm) REVERT: L 66 LYS cc_start: 0.6015 (mmtt) cc_final: 0.5812 (mmtt) REVERT: L 98 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7291 (tm-30) REVERT: L 145 ASP cc_start: 0.7797 (t70) cc_final: 0.7445 (m-30) REVERT: L 175 PHE cc_start: 0.8288 (p90) cc_final: 0.7848 (p90) REVERT: L 301 ASP cc_start: 0.7743 (m-30) cc_final: 0.7533 (m-30) REVERT: L 339 TRP cc_start: 0.8502 (t-100) cc_final: 0.8275 (t-100) REVERT: L 353 SER cc_start: 0.9572 (p) cc_final: 0.9289 (t) REVERT: L 367 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7040 (tp30) REVERT: L 393 LEU cc_start: 0.9327 (mt) cc_final: 0.8523 (tt) REVERT: M 12 PHE cc_start: 0.7578 (m-80) cc_final: 0.6674 (m-80) REVERT: M 21 ASP cc_start: 0.7439 (p0) cc_final: 0.7042 (p0) REVERT: M 41 MET cc_start: 0.8946 (mmm) cc_final: 0.8302 (mmm) REVERT: M 166 ASP cc_start: 0.7589 (t0) cc_final: 0.7365 (t0) REVERT: M 195 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8507 (tp-100) REVERT: M 212 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7911 (mm-40) REVERT: M 213 SER cc_start: 0.8774 (m) cc_final: 0.8299 (p) REVERT: M 296 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7804 (mt-10) REVERT: M 321 PHE cc_start: 0.8473 (p90) cc_final: 0.7922 (p90) REVERT: M 393 LEU cc_start: 0.9372 (mt) cc_final: 0.8810 (tt) REVERT: N 21 ASP cc_start: 0.7437 (p0) cc_final: 0.6834 (p0) REVERT: N 41 MET cc_start: 0.8999 (mmm) cc_final: 0.8595 (mmm) REVERT: N 213 SER cc_start: 0.8515 (t) cc_final: 0.8155 (p) REVERT: N 339 TRP cc_start: 0.8540 (t-100) cc_final: 0.8259 (t-100) REVERT: N 344 VAL cc_start: 0.9307 (t) cc_final: 0.8570 (t) REVERT: N 353 SER cc_start: 0.9595 (p) cc_final: 0.9284 (t) REVERT: N 367 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6995 (tp30) REVERT: N 393 LEU cc_start: 0.9307 (mt) cc_final: 0.8539 (tt) outliers start: 1 outliers final: 0 residues processed: 1105 average time/residue: 1.0094 time to fit residues: 1859.0454 Evaluate side-chains 1007 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1007 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 325 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 314 optimal weight: 0.0670 chunk 158 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 334 optimal weight: 0.8980 chunk 358 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 413 optimal weight: 3.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 340 ASN ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44142 Z= 0.226 Angle : 0.588 7.696 60277 Z= 0.310 Chirality : 0.043 0.165 6251 Planarity : 0.007 0.143 7924 Dihedral : 5.533 47.254 5992 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.50 % Favored : 88.67 % Rotamer: Outliers : 0.02 % Allowed : 0.55 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 2.17 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 5418 helix: -0.24 (0.17), residues: 903 sheet: -0.49 (0.13), residues: 1722 loop : -2.20 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 203 HIS 0.012 0.001 HIS N 186 PHE 0.014 0.001 PHE A 308 TYR 0.018 0.001 TYR M 348 ARG 0.008 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1072 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1071 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.3520 (mmtt) cc_final: 0.2793 (mmtm) REVERT: A 186 HIS cc_start: 0.8530 (m-70) cc_final: 0.8247 (m-70) REVERT: A 296 GLU cc_start: 0.7340 (pt0) cc_final: 0.6825 (pt0) REVERT: A 321 PHE cc_start: 0.8961 (p90) cc_final: 0.8697 (p90) REVERT: B 41 MET cc_start: 0.7957 (mmm) cc_final: 0.7414 (tpp) REVERT: B 162 TYR cc_start: 0.7935 (t80) cc_final: 0.7671 (t80) REVERT: B 167 LYS cc_start: 0.3834 (mmtt) cc_final: 0.3185 (mtpp) REVERT: B 209 ASP cc_start: 0.6994 (m-30) cc_final: 0.6759 (m-30) REVERT: C 41 MET cc_start: 0.8083 (mmm) cc_final: 0.7089 (tpp) REVERT: C 167 LYS cc_start: 0.4015 (mmtt) cc_final: 0.3413 (mtpp) REVERT: C 294 LYS cc_start: 0.9242 (tttt) cc_final: 0.8951 (tttt) REVERT: C 331 THR cc_start: 0.4062 (p) cc_final: 0.3788 (p) REVERT: C 384 THR cc_start: 0.7668 (p) cc_final: 0.6834 (p) REVERT: D 41 MET cc_start: 0.7601 (mmm) cc_final: 0.6926 (tpp) REVERT: D 50 LEU cc_start: 0.8890 (mt) cc_final: 0.8450 (mp) REVERT: D 57 MET cc_start: 0.7321 (mtp) cc_final: 0.7017 (mtp) REVERT: D 100 ASP cc_start: 0.9128 (m-30) cc_final: 0.8634 (m-30) REVERT: D 167 LYS cc_start: 0.3539 (mmtt) cc_final: 0.2717 (mtpp) REVERT: D 296 GLU cc_start: 0.7304 (pt0) cc_final: 0.6961 (pt0) REVERT: D 384 THR cc_start: 0.7988 (p) cc_final: 0.7265 (p) REVERT: E 50 LEU cc_start: 0.8778 (mt) cc_final: 0.8195 (mp) REVERT: E 57 MET cc_start: 0.7038 (mtp) cc_final: 0.6593 (mtp) REVERT: E 93 ILE cc_start: 0.8354 (mm) cc_final: 0.8089 (mm) REVERT: E 167 LYS cc_start: 0.3536 (mmtt) cc_final: 0.3064 (mttt) REVERT: E 180 ASP cc_start: 0.8355 (m-30) cc_final: 0.8142 (m-30) REVERT: E 296 GLU cc_start: 0.7376 (pt0) cc_final: 0.7039 (pt0) REVERT: E 321 PHE cc_start: 0.8746 (p90) cc_final: 0.8528 (p90) REVERT: F 29 GLU cc_start: 0.8661 (mp0) cc_final: 0.8398 (mm-30) REVERT: F 41 MET cc_start: 0.8422 (mmm) cc_final: 0.7808 (tpp) REVERT: F 42 MET cc_start: 0.8098 (mtp) cc_final: 0.7749 (mtp) REVERT: F 167 LYS cc_start: 0.4435 (mmtt) cc_final: 0.3892 (mmtm) REVERT: F 294 LYS cc_start: 0.9112 (tttt) cc_final: 0.8909 (tttt) REVERT: F 296 GLU cc_start: 0.7369 (pt0) cc_final: 0.6910 (pt0) REVERT: F 348 TYR cc_start: 0.9183 (t80) cc_final: 0.8947 (t80) REVERT: F 413 ASN cc_start: 0.9350 (m-40) cc_final: 0.8818 (m-40) REVERT: G 41 MET cc_start: 0.8354 (mmm) cc_final: 0.7808 (tpp) REVERT: G 42 MET cc_start: 0.7370 (mtp) cc_final: 0.7062 (mtp) REVERT: G 93 ILE cc_start: 0.8273 (mm) cc_final: 0.8056 (mm) REVERT: G 155 ASN cc_start: 0.8528 (t0) cc_final: 0.8188 (t0) REVERT: G 321 PHE cc_start: 0.8898 (p90) cc_final: 0.8598 (p90) REVERT: G 322 LEU cc_start: 0.8403 (tp) cc_final: 0.8023 (mp) REVERT: H 12 PHE cc_start: 0.7586 (m-80) cc_final: 0.7006 (m-80) REVERT: H 41 MET cc_start: 0.8845 (mmm) cc_final: 0.8029 (mmt) REVERT: H 98 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7774 (tm-30) REVERT: H 167 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7876 (mtmm) REVERT: H 175 PHE cc_start: 0.8735 (p90) cc_final: 0.8166 (p90) REVERT: H 186 HIS cc_start: 0.8645 (t70) cc_final: 0.8246 (t-170) REVERT: H 213 SER cc_start: 0.8626 (t) cc_final: 0.8351 (p) REVERT: H 393 LEU cc_start: 0.9185 (mt) cc_final: 0.8544 (tt) REVERT: I 21 ASP cc_start: 0.7907 (p0) cc_final: 0.7354 (p0) REVERT: I 41 MET cc_start: 0.8729 (mmm) cc_final: 0.8106 (mtt) REVERT: I 42 MET cc_start: 0.7063 (ptp) cc_final: 0.6741 (ptp) REVERT: I 98 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7576 (tm-30) REVERT: I 175 PHE cc_start: 0.8492 (p90) cc_final: 0.7908 (p90) REVERT: I 186 HIS cc_start: 0.8697 (t-90) cc_final: 0.8292 (t70) REVERT: I 195 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8301 (tp-100) REVERT: I 212 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8122 (mm-40) REVERT: I 213 SER cc_start: 0.8892 (t) cc_final: 0.8544 (p) REVERT: I 353 SER cc_start: 0.9651 (p) cc_final: 0.9438 (t) REVERT: I 393 LEU cc_start: 0.9443 (mt) cc_final: 0.8703 (tt) REVERT: J 21 ASP cc_start: 0.7433 (p0) cc_final: 0.6917 (p0) REVERT: J 41 MET cc_start: 0.8954 (mmm) cc_final: 0.8551 (mmm) REVERT: J 42 MET cc_start: 0.7064 (pmm) cc_final: 0.6840 (pmm) REVERT: J 175 PHE cc_start: 0.8371 (p90) cc_final: 0.8007 (p90) REVERT: J 186 HIS cc_start: 0.8574 (t-90) cc_final: 0.8280 (t70) REVERT: J 393 LEU cc_start: 0.9331 (mt) cc_final: 0.8601 (tt) REVERT: K 12 PHE cc_start: 0.7741 (m-80) cc_final: 0.7064 (m-80) REVERT: K 41 MET cc_start: 0.9081 (mmm) cc_final: 0.8581 (mmm) REVERT: K 95 ASP cc_start: 0.8937 (t0) cc_final: 0.8733 (t0) REVERT: K 175 PHE cc_start: 0.8261 (p90) cc_final: 0.8050 (p90) REVERT: K 186 HIS cc_start: 0.8548 (t-90) cc_final: 0.8221 (t70) REVERT: K 213 SER cc_start: 0.8633 (m) cc_final: 0.8228 (p) REVERT: K 393 LEU cc_start: 0.9230 (mt) cc_final: 0.8296 (tt) REVERT: L 21 ASP cc_start: 0.8274 (p0) cc_final: 0.7705 (p0) REVERT: L 41 MET cc_start: 0.8716 (mmm) cc_final: 0.8408 (mmm) REVERT: L 145 ASP cc_start: 0.7876 (t70) cc_final: 0.7469 (m-30) REVERT: L 175 PHE cc_start: 0.8202 (p90) cc_final: 0.7845 (p90) REVERT: L 301 ASP cc_start: 0.8021 (m-30) cc_final: 0.7741 (m-30) REVERT: L 353 SER cc_start: 0.9575 (p) cc_final: 0.9283 (t) REVERT: L 393 LEU cc_start: 0.9342 (mt) cc_final: 0.8569 (tt) REVERT: M 12 PHE cc_start: 0.7687 (m-80) cc_final: 0.7046 (m-80) REVERT: M 21 ASP cc_start: 0.7588 (p0) cc_final: 0.7255 (p0) REVERT: M 41 MET cc_start: 0.8963 (mmm) cc_final: 0.8346 (mmm) REVERT: M 45 TRP cc_start: 0.8142 (m100) cc_final: 0.7638 (m100) REVERT: M 166 ASP cc_start: 0.8064 (t0) cc_final: 0.7746 (t0) REVERT: M 175 PHE cc_start: 0.8621 (p90) cc_final: 0.8304 (p90) REVERT: M 212 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7929 (mm-40) REVERT: M 296 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7929 (mt-10) REVERT: M 321 PHE cc_start: 0.8545 (p90) cc_final: 0.7941 (p90) REVERT: M 393 LEU cc_start: 0.9385 (mt) cc_final: 0.8843 (tt) REVERT: N 21 ASP cc_start: 0.7478 (p0) cc_final: 0.6872 (p0) REVERT: N 41 MET cc_start: 0.8967 (mmm) cc_final: 0.8585 (mmm) REVERT: N 138 GLU cc_start: 0.8841 (tp30) cc_final: 0.8327 (tp30) REVERT: N 175 PHE cc_start: 0.8385 (p90) cc_final: 0.8133 (p90) REVERT: N 207 ASP cc_start: 0.8369 (m-30) cc_final: 0.8137 (m-30) REVERT: N 213 SER cc_start: 0.8586 (t) cc_final: 0.8245 (p) REVERT: N 393 LEU cc_start: 0.9339 (mt) cc_final: 0.8470 (tt) outliers start: 1 outliers final: 0 residues processed: 1072 average time/residue: 1.0149 time to fit residues: 1820.6621 Evaluate side-chains 988 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 988 time to evaluate : 4.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 478 optimal weight: 8.9990 chunk 504 optimal weight: 5.9990 chunk 459 optimal weight: 6.9990 chunk 490 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 385 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 443 optimal weight: 6.9990 chunk 463 optimal weight: 0.9980 chunk 488 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 340 ASN G 132 HIS ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN M 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44142 Z= 0.210 Angle : 0.573 7.794 60277 Z= 0.304 Chirality : 0.043 0.150 6251 Planarity : 0.007 0.124 7924 Dihedral : 5.417 45.834 5992 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.65 % Favored : 88.58 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 1.86 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.11), residues: 5418 helix: 0.02 (0.18), residues: 882 sheet: -0.60 (0.13), residues: 1708 loop : -2.07 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 371 HIS 0.013 0.001 HIS A 107 PHE 0.019 0.001 PHE B 321 TYR 0.017 0.001 TYR N 348 ARG 0.009 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1077 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1076 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.3542 (mmtt) cc_final: 0.2827 (mmtm) REVERT: A 186 HIS cc_start: 0.8527 (m-70) cc_final: 0.8250 (m-70) REVERT: A 296 GLU cc_start: 0.7374 (pt0) cc_final: 0.6878 (pt0) REVERT: A 321 PHE cc_start: 0.8972 (p90) cc_final: 0.8716 (p90) REVERT: B 41 MET cc_start: 0.7766 (mmm) cc_final: 0.7231 (tpp) REVERT: B 100 ASP cc_start: 0.9115 (m-30) cc_final: 0.8778 (m-30) REVERT: B 162 TYR cc_start: 0.7917 (t80) cc_final: 0.7696 (t80) REVERT: B 167 LYS cc_start: 0.3712 (mmtt) cc_final: 0.3021 (mtpp) REVERT: B 216 ASP cc_start: 0.7981 (m-30) cc_final: 0.7715 (m-30) REVERT: C 41 MET cc_start: 0.8089 (mmm) cc_final: 0.7190 (tpp) REVERT: C 108 ASP cc_start: 0.7756 (t0) cc_final: 0.7521 (t0) REVERT: C 167 LYS cc_start: 0.4013 (mmtt) cc_final: 0.3639 (mmtt) REVERT: C 294 LYS cc_start: 0.9268 (tttt) cc_final: 0.8943 (tttt) REVERT: C 331 THR cc_start: 0.4054 (p) cc_final: 0.3813 (p) REVERT: C 384 THR cc_start: 0.7598 (p) cc_final: 0.6806 (p) REVERT: D 41 MET cc_start: 0.7527 (mmm) cc_final: 0.7084 (tpp) REVERT: D 57 MET cc_start: 0.7256 (mtp) cc_final: 0.6933 (mtp) REVERT: D 100 ASP cc_start: 0.9095 (m-30) cc_final: 0.8591 (m-30) REVERT: D 167 LYS cc_start: 0.3565 (mmtt) cc_final: 0.2860 (mtpp) REVERT: D 296 GLU cc_start: 0.7315 (pt0) cc_final: 0.6900 (pt0) REVERT: D 384 THR cc_start: 0.7902 (p) cc_final: 0.7179 (p) REVERT: E 50 LEU cc_start: 0.8772 (mt) cc_final: 0.8224 (mp) REVERT: E 57 MET cc_start: 0.6963 (mtp) cc_final: 0.6712 (mtp) REVERT: E 93 ILE cc_start: 0.8410 (mm) cc_final: 0.8152 (mm) REVERT: E 167 LYS cc_start: 0.3466 (mmtt) cc_final: 0.2955 (mttt) REVERT: E 296 GLU cc_start: 0.7344 (pt0) cc_final: 0.7038 (pt0) REVERT: E 321 PHE cc_start: 0.8751 (p90) cc_final: 0.8520 (p90) REVERT: F 29 GLU cc_start: 0.8626 (mp0) cc_final: 0.8336 (mm-30) REVERT: F 41 MET cc_start: 0.8394 (mmm) cc_final: 0.7757 (tpp) REVERT: F 42 MET cc_start: 0.8179 (mtp) cc_final: 0.7848 (mtp) REVERT: F 167 LYS cc_start: 0.4410 (mmtt) cc_final: 0.4199 (mmtm) REVERT: F 216 ASP cc_start: 0.7812 (m-30) cc_final: 0.7577 (m-30) REVERT: F 348 TYR cc_start: 0.9198 (t80) cc_final: 0.8985 (t80) REVERT: G 41 MET cc_start: 0.8316 (mmm) cc_final: 0.7768 (tpp) REVERT: G 42 MET cc_start: 0.7383 (mtp) cc_final: 0.7099 (mtp) REVERT: G 93 ILE cc_start: 0.8256 (mm) cc_final: 0.7965 (mm) REVERT: G 155 ASN cc_start: 0.8592 (t0) cc_final: 0.8260 (t0) REVERT: G 321 PHE cc_start: 0.8879 (p90) cc_final: 0.8554 (p90) REVERT: G 322 LEU cc_start: 0.8433 (tp) cc_final: 0.8020 (mp) REVERT: G 331 THR cc_start: 0.4171 (p) cc_final: 0.3963 (p) REVERT: H 12 PHE cc_start: 0.7538 (m-80) cc_final: 0.7012 (m-80) REVERT: H 41 MET cc_start: 0.8813 (mmm) cc_final: 0.7863 (mmt) REVERT: H 98 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7835 (tm-30) REVERT: H 170 ILE cc_start: 0.8278 (mt) cc_final: 0.7971 (mt) REVERT: H 175 PHE cc_start: 0.8761 (p90) cc_final: 0.8248 (p90) REVERT: H 186 HIS cc_start: 0.8766 (t70) cc_final: 0.8291 (t-170) REVERT: H 213 SER cc_start: 0.8654 (t) cc_final: 0.8413 (p) REVERT: H 393 LEU cc_start: 0.9224 (mt) cc_final: 0.8500 (tt) REVERT: I 21 ASP cc_start: 0.7935 (p0) cc_final: 0.7372 (p0) REVERT: I 41 MET cc_start: 0.8718 (mmm) cc_final: 0.8115 (mtt) REVERT: I 42 MET cc_start: 0.7068 (ptp) cc_final: 0.6784 (ptp) REVERT: I 98 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7608 (tm-30) REVERT: I 175 PHE cc_start: 0.8602 (p90) cc_final: 0.8094 (p90) REVERT: I 186 HIS cc_start: 0.8681 (t-90) cc_final: 0.8300 (t-170) REVERT: I 195 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8278 (tp-100) REVERT: I 212 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8409 (mm-40) REVERT: I 213 SER cc_start: 0.8816 (t) cc_final: 0.8546 (p) REVERT: I 353 SER cc_start: 0.9650 (p) cc_final: 0.9447 (t) REVERT: I 393 LEU cc_start: 0.9419 (mt) cc_final: 0.8742 (tt) REVERT: J 21 ASP cc_start: 0.7123 (p0) cc_final: 0.6772 (p0) REVERT: J 41 MET cc_start: 0.8939 (mmm) cc_final: 0.8443 (mmm) REVERT: J 175 PHE cc_start: 0.8483 (p90) cc_final: 0.8007 (p90) REVERT: J 186 HIS cc_start: 0.8550 (t-90) cc_final: 0.8284 (t70) REVERT: J 393 LEU cc_start: 0.9302 (mt) cc_final: 0.8745 (tt) REVERT: K 12 PHE cc_start: 0.7747 (m-80) cc_final: 0.7021 (m-80) REVERT: K 41 MET cc_start: 0.9108 (mmm) cc_final: 0.8618 (mmm) REVERT: K 186 HIS cc_start: 0.8465 (t-90) cc_final: 0.8122 (t70) REVERT: K 195 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8584 (tp-100) REVERT: K 213 SER cc_start: 0.8168 (m) cc_final: 0.7818 (p) REVERT: K 367 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7352 (tp30) REVERT: K 393 LEU cc_start: 0.9213 (mt) cc_final: 0.8380 (tt) REVERT: L 21 ASP cc_start: 0.7895 (p0) cc_final: 0.7454 (p0) REVERT: L 41 MET cc_start: 0.8700 (mmm) cc_final: 0.8413 (mmm) REVERT: L 145 ASP cc_start: 0.7845 (t70) cc_final: 0.7482 (m-30) REVERT: L 175 PHE cc_start: 0.8159 (p90) cc_final: 0.7782 (p90) REVERT: L 195 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8175 (tp-100) REVERT: L 301 ASP cc_start: 0.7997 (m-30) cc_final: 0.7714 (m-30) REVERT: L 353 SER cc_start: 0.9581 (p) cc_final: 0.9257 (t) REVERT: L 393 LEU cc_start: 0.9353 (mt) cc_final: 0.8596 (tt) REVERT: M 12 PHE cc_start: 0.7547 (m-80) cc_final: 0.6860 (m-80) REVERT: M 21 ASP cc_start: 0.7574 (p0) cc_final: 0.7249 (p0) REVERT: M 64 GLU cc_start: 0.7930 (pt0) cc_final: 0.7460 (pt0) REVERT: M 166 ASP cc_start: 0.8069 (t0) cc_final: 0.7768 (t0) REVERT: M 175 PHE cc_start: 0.8611 (p90) cc_final: 0.8205 (p90) REVERT: M 185 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8212 (tttt) REVERT: M 186 HIS cc_start: 0.8381 (t70) cc_final: 0.8059 (t70) REVERT: M 212 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7929 (mm-40) REVERT: M 213 SER cc_start: 0.8809 (m) cc_final: 0.8325 (p) REVERT: M 296 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8134 (mt-10) REVERT: M 321 PHE cc_start: 0.8531 (p90) cc_final: 0.8038 (p90) REVERT: M 393 LEU cc_start: 0.9393 (mt) cc_final: 0.8854 (tt) REVERT: N 21 ASP cc_start: 0.7528 (p0) cc_final: 0.6969 (p0) REVERT: N 41 MET cc_start: 0.8941 (mmm) cc_final: 0.8557 (mmm) REVERT: N 138 GLU cc_start: 0.8817 (tp30) cc_final: 0.8266 (tp30) REVERT: N 175 PHE cc_start: 0.8511 (p90) cc_final: 0.8218 (p90) REVERT: N 213 SER cc_start: 0.8595 (t) cc_final: 0.8258 (p) REVERT: N 393 LEU cc_start: 0.9346 (mt) cc_final: 0.8650 (tt) outliers start: 1 outliers final: 0 residues processed: 1077 average time/residue: 0.9665 time to fit residues: 1726.9502 Evaluate side-chains 989 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 989 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 322 optimal weight: 5.9990 chunk 518 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 360 optimal weight: 6.9990 chunk 543 optimal weight: 8.9990 chunk 500 optimal weight: 0.0060 chunk 433 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 334 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN F 186 HIS G 132 HIS ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44142 Z= 0.169 Angle : 0.555 12.804 60277 Z= 0.291 Chirality : 0.043 0.159 6251 Planarity : 0.006 0.161 7924 Dihedral : 5.222 44.565 5992 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.01 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 1.24 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.11), residues: 5418 helix: 0.27 (0.18), residues: 875 sheet: -0.58 (0.12), residues: 1855 loop : -2.05 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 371 HIS 0.014 0.001 HIS A 107 PHE 0.018 0.001 PHE C 308 TYR 0.016 0.001 TYR G 23 ARG 0.005 0.000 ARG B 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10836 Ramachandran restraints generated. 5418 Oldfield, 0 Emsley, 5418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1079 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1079 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8849 (t0) cc_final: 0.8604 (t0) REVERT: A 167 LYS cc_start: 0.3680 (mmtt) cc_final: 0.2922 (mmtm) REVERT: A 186 HIS cc_start: 0.8484 (m-70) cc_final: 0.8224 (m-70) REVERT: A 296 GLU cc_start: 0.7336 (pt0) cc_final: 0.6831 (pt0) REVERT: A 321 PHE cc_start: 0.8927 (p90) cc_final: 0.8631 (p90) REVERT: B 41 MET cc_start: 0.7777 (mmm) cc_final: 0.7283 (tpp) REVERT: B 100 ASP cc_start: 0.9107 (m-30) cc_final: 0.8832 (m-30) REVERT: B 162 TYR cc_start: 0.7853 (t80) cc_final: 0.7609 (t80) REVERT: B 167 LYS cc_start: 0.3636 (mmtt) cc_final: 0.2961 (mtpp) REVERT: C 41 MET cc_start: 0.8063 (mmm) cc_final: 0.7184 (tpp) REVERT: C 42 MET cc_start: 0.7579 (mtp) cc_final: 0.7343 (mmt) REVERT: C 108 ASP cc_start: 0.7704 (t0) cc_final: 0.7486 (t0) REVERT: C 167 LYS cc_start: 0.3758 (mmtt) cc_final: 0.3264 (mmtt) REVERT: C 294 LYS cc_start: 0.9212 (tttt) cc_final: 0.8900 (tttt) REVERT: C 331 THR cc_start: 0.3815 (p) cc_final: 0.3599 (p) REVERT: C 384 THR cc_start: 0.7476 (p) cc_final: 0.6626 (p) REVERT: D 22 LYS cc_start: 0.7819 (pttm) cc_final: 0.7202 (ptmt) REVERT: D 41 MET cc_start: 0.7520 (mmm) cc_final: 0.7026 (tpp) REVERT: D 57 MET cc_start: 0.7073 (mtp) cc_final: 0.6815 (mtp) REVERT: D 100 ASP cc_start: 0.9052 (m-30) cc_final: 0.8814 (m-30) REVERT: D 167 LYS cc_start: 0.3291 (mmtt) cc_final: 0.2596 (mttm) REVERT: D 296 GLU cc_start: 0.7363 (pt0) cc_final: 0.6963 (pt0) REVERT: D 384 THR cc_start: 0.7831 (p) cc_final: 0.7112 (p) REVERT: E 50 LEU cc_start: 0.8788 (mt) cc_final: 0.8165 (mp) REVERT: E 93 ILE cc_start: 0.8377 (mm) cc_final: 0.8099 (mm) REVERT: E 167 LYS cc_start: 0.3304 (mmtt) cc_final: 0.2788 (mttt) REVERT: E 296 GLU cc_start: 0.7294 (pt0) cc_final: 0.7069 (pt0) REVERT: E 321 PHE cc_start: 0.8722 (p90) cc_final: 0.8490 (p90) REVERT: F 29 GLU cc_start: 0.8598 (mp0) cc_final: 0.8351 (mm-30) REVERT: F 41 MET cc_start: 0.8285 (mmm) cc_final: 0.7748 (tpp) REVERT: F 42 MET cc_start: 0.8102 (mtp) cc_final: 0.7762 (mtp) REVERT: F 167 LYS cc_start: 0.4426 (mmtt) cc_final: 0.4110 (mmtm) REVERT: F 348 TYR cc_start: 0.9193 (t80) cc_final: 0.8962 (t80) REVERT: F 413 ASN cc_start: 0.9289 (m-40) cc_final: 0.8959 (m-40) REVERT: G 41 MET cc_start: 0.8302 (mmm) cc_final: 0.7671 (tpp) REVERT: G 42 MET cc_start: 0.7449 (mtp) cc_final: 0.7145 (mtp) REVERT: G 93 ILE cc_start: 0.8227 (mm) cc_final: 0.7944 (mm) REVERT: G 155 ASN cc_start: 0.8593 (t0) cc_final: 0.8256 (t0) REVERT: G 294 LYS cc_start: 0.9092 (ptmt) cc_final: 0.8872 (ptpt) REVERT: G 321 PHE cc_start: 0.8828 (p90) cc_final: 0.8562 (p90) REVERT: G 322 LEU cc_start: 0.8361 (tp) cc_final: 0.8008 (mp) REVERT: H 12 PHE cc_start: 0.7539 (m-80) cc_final: 0.7012 (m-80) REVERT: H 41 MET cc_start: 0.8789 (mmm) cc_final: 0.7874 (mmt) REVERT: H 98 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7642 (tm-30) REVERT: H 175 PHE cc_start: 0.8738 (p90) cc_final: 0.8172 (p90) REVERT: H 186 HIS cc_start: 0.8739 (t70) cc_final: 0.8294 (t-170) REVERT: H 213 SER cc_start: 0.8614 (t) cc_final: 0.8382 (p) REVERT: H 367 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7218 (tp30) REVERT: H 393 LEU cc_start: 0.9208 (mt) cc_final: 0.8516 (tt) REVERT: I 21 ASP cc_start: 0.7899 (p0) cc_final: 0.7316 (p0) REVERT: I 41 MET cc_start: 0.8690 (mmm) cc_final: 0.8487 (mmm) REVERT: I 62 ASN cc_start: 0.7578 (t0) cc_final: 0.7339 (t0) REVERT: I 98 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7390 (tm-30) REVERT: I 175 PHE cc_start: 0.8507 (p90) cc_final: 0.8029 (p90) REVERT: I 186 HIS cc_start: 0.8651 (t-90) cc_final: 0.8243 (t70) REVERT: I 195 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8249 (tp-100) REVERT: I 212 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8289 (mm-40) REVERT: I 213 SER cc_start: 0.8681 (t) cc_final: 0.8331 (p) REVERT: I 353 SER cc_start: 0.9629 (p) cc_final: 0.9390 (t) REVERT: I 393 LEU cc_start: 0.9456 (mt) cc_final: 0.8767 (tt) REVERT: J 21 ASP cc_start: 0.7171 (p0) cc_final: 0.6847 (p0) REVERT: J 41 MET cc_start: 0.8933 (mmm) cc_final: 0.8473 (mmm) REVERT: J 140 MET cc_start: 0.8247 (mmt) cc_final: 0.7772 (mmt) REVERT: J 175 PHE cc_start: 0.8386 (p90) cc_final: 0.7965 (p90) REVERT: J 186 HIS cc_start: 0.8601 (t-90) cc_final: 0.8246 (t70) REVERT: J 393 LEU cc_start: 0.9275 (mt) cc_final: 0.8751 (tt) REVERT: K 21 ASP cc_start: 0.7935 (p0) cc_final: 0.7311 (p0) REVERT: K 41 MET cc_start: 0.9079 (mmm) cc_final: 0.8656 (mmm) REVERT: K 138 GLU cc_start: 0.8572 (tp30) cc_final: 0.8086 (tp30) REVERT: K 175 PHE cc_start: 0.8434 (p90) cc_final: 0.8145 (p90) REVERT: K 186 HIS cc_start: 0.8536 (t-90) cc_final: 0.8140 (t70) REVERT: K 195 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8429 (tp-100) REVERT: K 367 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7315 (tp30) REVERT: K 393 LEU cc_start: 0.9245 (mt) cc_final: 0.8364 (tt) REVERT: L 21 ASP cc_start: 0.7830 (p0) cc_final: 0.7384 (p0) REVERT: L 41 MET cc_start: 0.8760 (mmm) cc_final: 0.8455 (mmm) REVERT: L 145 ASP cc_start: 0.7824 (t70) cc_final: 0.7506 (m-30) REVERT: L 175 PHE cc_start: 0.8265 (p90) cc_final: 0.7773 (p90) REVERT: L 195 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8076 (tp-100) REVERT: L 301 ASP cc_start: 0.7966 (m-30) cc_final: 0.7705 (m-30) REVERT: L 353 SER cc_start: 0.9575 (p) cc_final: 0.9244 (t) REVERT: L 367 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7096 (tp30) REVERT: L 393 LEU cc_start: 0.9336 (mt) cc_final: 0.8666 (tt) REVERT: M 12 PHE cc_start: 0.7526 (m-80) cc_final: 0.6809 (m-80) REVERT: M 21 ASP cc_start: 0.7513 (p0) cc_final: 0.7202 (p0) REVERT: M 166 ASP cc_start: 0.8066 (t0) cc_final: 0.7773 (t0) REVERT: M 175 PHE cc_start: 0.8584 (p90) cc_final: 0.8167 (p90) REVERT: M 185 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8299 (tttt) REVERT: M 186 HIS cc_start: 0.8333 (t70) cc_final: 0.7917 (t70) REVERT: M 212 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8131 (mm-40) REVERT: M 213 SER cc_start: 0.8739 (m) cc_final: 0.8293 (p) REVERT: M 296 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8069 (mt-10) REVERT: M 321 PHE cc_start: 0.8432 (p90) cc_final: 0.8015 (p90) REVERT: M 393 LEU cc_start: 0.9377 (mt) cc_final: 0.8856 (tt) REVERT: N 41 MET cc_start: 0.8872 (mmm) cc_final: 0.8514 (mmm) REVERT: N 138 GLU cc_start: 0.8766 (tp30) cc_final: 0.8215 (tp30) REVERT: N 175 PHE cc_start: 0.8485 (p90) cc_final: 0.8199 (p90) REVERT: N 195 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8488 (tp-100) REVERT: N 213 SER cc_start: 0.8539 (t) cc_final: 0.8224 (p) REVERT: N 353 SER cc_start: 0.9482 (p) cc_final: 0.9034 (t) REVERT: N 393 LEU cc_start: 0.9328 (mt) cc_final: 0.8659 (tt) outliers start: 0 outliers final: 0 residues processed: 1079 average time/residue: 0.9802 time to fit residues: 1756.9802 Evaluate side-chains 991 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 991 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 344 optimal weight: 5.9990 chunk 461 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 399 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 433 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 445 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS G 132 HIS ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125514 restraints weight = 215326.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128665 restraints weight = 112649.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130845 restraints weight = 71200.799| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44142 Z= 0.195 Angle : 0.561 9.323 60277 Z= 0.292 Chirality : 0.043 0.149 6251 Planarity : 0.007 0.145 7924 Dihedral : 5.190 43.680 5992 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.54 % Favored : 88.69 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.55 % Twisted Proline : 0.93 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 5418 helix: 0.33 (0.18), residues: 875 sheet: -0.50 (0.13), residues: 1708 loop : -1.99 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 371 HIS 0.009 0.001 HIS B 107 PHE 0.016 0.001 PHE D 308 TYR 0.014 0.001 TYR L 221 ARG 0.007 0.000 ARG B 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27260.79 seconds wall clock time: 470 minutes 5.76 seconds (28205.76 seconds total)