Starting phenix.real_space_refine on Sat Feb 24 06:25:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl0_10233/02_2024/6sl0_10233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl0_10233/02_2024/6sl0_10233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl0_10233/02_2024/6sl0_10233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl0_10233/02_2024/6sl0_10233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl0_10233/02_2024/6sl0_10233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl0_10233/02_2024/6sl0_10233_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 190 5.16 5 C 26604 2.51 5 N 7286 2.21 5 O 7772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 947": "NH1" <-> "NH2" Residue "A PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A ASP 996": "OD1" <-> "OD2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1004": "OD1" <-> "OD2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1287": "NH1" <-> "NH2" Residue "A PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1379": "OE1" <-> "OE2" Residue "A ARG 1461": "NH1" <-> "NH2" Residue "A TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1468": "NH1" <-> "NH2" Residue "A PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1694": "OE1" <-> "OE2" Residue "A TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A PHE 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1857": "OE1" <-> "OE2" Residue "A ASP 1862": "OD1" <-> "OD2" Residue "A ARG 1863": "NH1" <-> "NH2" Residue "A ARG 1880": "NH1" <-> "NH2" Residue "A TYR 1931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1945": "NH1" <-> "NH2" Residue "A TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1959": "NH1" <-> "NH2" Residue "A TYR 1963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2019": "NH1" <-> "NH2" Residue "A ARG 2056": "NH1" <-> "NH2" Residue "A ARG 2068": "NH1" <-> "NH2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "A GLU 2113": "OE1" <-> "OE2" Residue "A ARG 2115": "NH1" <-> "NH2" Residue "A ARG 2123": "NH1" <-> "NH2" Residue "A ARG 2134": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2173": "NH1" <-> "NH2" Residue "A ARG 2176": "NH1" <-> "NH2" Residue "A ARG 2178": "NH1" <-> "NH2" Residue "A ASP 2216": "OD1" <-> "OD2" Residue "A GLU 2219": "OE1" <-> "OE2" Residue "A ARG 2225": "NH1" <-> "NH2" Residue "A ARG 2245": "NH1" <-> "NH2" Residue "A TYR 2254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2260": "NH1" <-> "NH2" Residue "A ARG 2286": "NH1" <-> "NH2" Residue "A ARG 2314": "NH1" <-> "NH2" Residue "A ARG 2364": "NH1" <-> "NH2" Residue "A ARG 2365": "NH1" <-> "NH2" Residue "A ARG 2370": "NH1" <-> "NH2" Residue "A ASP 2394": "OD1" <-> "OD2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2425": "NH1" <-> "NH2" Residue "A PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2455": "NH1" <-> "NH2" Residue "A ARG 2473": "NH1" <-> "NH2" Residue "A ARG 2515": "NH1" <-> "NH2" Residue "A PHE 2579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2603": "NH1" <-> "NH2" Residue "A ARG 2617": "NH1" <-> "NH2" Residue "A ARG 2637": "NH1" <-> "NH2" Residue "A ARG 2640": "NH1" <-> "NH2" Residue "A ARG 2642": "NH1" <-> "NH2" Residue "A ARG 2647": "NH1" <-> "NH2" Residue "A TYR 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2662": "OE1" <-> "OE2" Residue "A ARG 2680": "NH1" <-> "NH2" Residue "A ARG 2706": "NH1" <-> "NH2" Residue "A TYR 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2711": "NH1" <-> "NH2" Residue "A ARG 2712": "NH1" <-> "NH2" Residue "A ARG 2716": "NH1" <-> "NH2" Residue "A ARG 2722": "NH1" <-> "NH2" Residue "A TYR 2723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2739": "NH1" <-> "NH2" Residue "A TYR 2742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2744": "NH1" <-> "NH2" Residue "A ARG 2761": "NH1" <-> "NH2" Residue "A ARG 2788": "NH1" <-> "NH2" Residue "A PHE 2798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2799": "NH1" <-> "NH2" Residue "A ARG 2818": "NH1" <-> "NH2" Residue "A ARG 2819": "NH1" <-> "NH2" Residue "A ARG 2829": "NH1" <-> "NH2" Residue "A ARG 2843": "NH1" <-> "NH2" Residue "A ARG 2901": "NH1" <-> "NH2" Residue "A TYR 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 721": "NH1" <-> "NH2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 854": "NH1" <-> "NH2" Residue "B ARG 891": "NH1" <-> "NH2" Residue "B TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 947": "NH1" <-> "NH2" Residue "B PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 970": "OE1" <-> "OE2" Residue "B TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B ASP 993": "OD1" <-> "OD2" Residue "B ASP 996": "OD1" <-> "OD2" Residue "B PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1004": "OD1" <-> "OD2" Residue "B PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "B TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "B PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1287": "NH1" <-> "NH2" Residue "B PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1379": "OE1" <-> "OE2" Residue "B ARG 1461": "NH1" <-> "NH2" Residue "B TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1468": "NH1" <-> "NH2" Residue "B PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1694": "OE1" <-> "OE2" Residue "B TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1769": "NH1" <-> "NH2" Residue "B PHE 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1857": "OE1" <-> "OE2" Residue "B ASP 1862": "OD1" <-> "OD2" Residue "B ARG 1863": "NH1" <-> "NH2" Residue "B ARG 1880": "NH1" <-> "NH2" Residue "B TYR 1931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1945": "NH1" <-> "NH2" Residue "B TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1959": "NH1" <-> "NH2" Residue "B TYR 1963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2019": "NH1" <-> "NH2" Residue "B ARG 2056": "NH1" <-> "NH2" Residue "B ARG 2068": "NH1" <-> "NH2" Residue "B ARG 2081": "NH1" <-> "NH2" Residue "B ARG 2100": "NH1" <-> "NH2" Residue "B GLU 2113": "OE1" <-> "OE2" Residue "B ARG 2115": "NH1" <-> "NH2" Residue "B ARG 2123": "NH1" <-> "NH2" Residue "B ARG 2134": "NH1" <-> "NH2" Residue "B ARG 2158": "NH1" <-> "NH2" Residue "B ARG 2163": "NH1" <-> "NH2" Residue "B ARG 2173": "NH1" <-> "NH2" Residue "B ARG 2176": "NH1" <-> "NH2" Residue "B ARG 2178": "NH1" <-> "NH2" Residue "B ASP 2216": "OD1" <-> "OD2" Residue "B GLU 2219": "OE1" <-> "OE2" Residue "B ARG 2225": "NH1" <-> "NH2" Residue "B ARG 2245": "NH1" <-> "NH2" Residue "B TYR 2254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2260": "NH1" <-> "NH2" Residue "B ARG 2286": "NH1" <-> "NH2" Residue "B ARG 2314": "NH1" <-> "NH2" Residue "B ARG 2364": "NH1" <-> "NH2" Residue "B ARG 2365": "NH1" <-> "NH2" Residue "B ARG 2370": "NH1" <-> "NH2" Residue "B ASP 2394": "OD1" <-> "OD2" Residue "B ARG 2397": "NH1" <-> "NH2" Residue "B ARG 2425": "NH1" <-> "NH2" Residue "B PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2455": "NH1" <-> "NH2" Residue "B ARG 2473": "NH1" <-> "NH2" Residue "B ARG 2515": "NH1" <-> "NH2" Residue "B PHE 2579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2603": "NH1" <-> "NH2" Residue "B ARG 2617": "NH1" <-> "NH2" Residue "B ARG 2637": "NH1" <-> "NH2" Residue "B ARG 2640": "NH1" <-> "NH2" Residue "B ARG 2642": "NH1" <-> "NH2" Residue "B ARG 2647": "NH1" <-> "NH2" Residue "B TYR 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2662": "OE1" <-> "OE2" Residue "B ARG 2680": "NH1" <-> "NH2" Residue "B ARG 2706": "NH1" <-> "NH2" Residue "B TYR 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2711": "NH1" <-> "NH2" Residue "B ARG 2712": "NH1" <-> "NH2" Residue "B ARG 2716": "NH1" <-> "NH2" Residue "B ARG 2722": "NH1" <-> "NH2" Residue "B TYR 2723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2739": "NH1" <-> "NH2" Residue "B TYR 2742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2744": "NH1" <-> "NH2" Residue "B ARG 2761": "NH1" <-> "NH2" Residue "B ARG 2788": "NH1" <-> "NH2" Residue "B PHE 2798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2799": "NH1" <-> "NH2" Residue "B ARG 2818": "NH1" <-> "NH2" Residue "B ARG 2819": "NH1" <-> "NH2" Residue "B ARG 2829": "NH1" <-> "NH2" Residue "B ARG 2843": "NH1" <-> "NH2" Residue "B ARG 2901": "NH1" <-> "NH2" Residue "B TYR 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41860 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2638, 20898 Classifications: {'peptide': 2638} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 111, 'TRANS': 2526} Chain breaks: 20 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 20898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2638, 20898 Classifications: {'peptide': 2638} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 111, 'TRANS': 2526} Chain breaks: 20 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.25, per 1000 atoms: 0.48 Number of scatterers: 41860 At special positions: 0 Unit cell: (212.859, 111.195, 203.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 190 16.00 P 6 15.00 Mg 2 11.99 O 7772 8.00 N 7286 7.00 C 26604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1447 " distance=2.05 Simple disulfide: pdb=" SG CYS B1408 " - pdb=" SG CYS B1447 " distance=2.05 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: 15.60 Conformation dependent library (CDL) restraints added in 8.0 seconds 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 274 helices and 6 sheets defined 65.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.37 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 26 through 39 WARNING: missing atoms! Processing helix chain 'A' and resid 56 through 72 Processing helix chain 'A' and resid 86 through 102 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.990A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.859A pdb=" N GLN A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 399 through 415 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 458 through 474 removed outlier: 4.196A pdb=" N ILE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Proline residue: A 469 - end of helix removed outlier: 4.137A pdb=" N HIS A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 498 through 513 removed outlier: 4.494A pdb=" N ILE A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 removed outlier: 6.145A pdb=" N SER A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 716 through 742 Proline residue: A 730 - end of helix removed outlier: 3.835A pdb=" N TRP A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 770 Processing helix chain 'A' and resid 784 through 802 Processing helix chain 'A' and resid 810 through 821 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 838 through 857 Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 900 through 920 Processing helix chain 'A' and resid 929 through 935 Processing helix chain 'A' and resid 945 through 955 removed outlier: 4.346A pdb=" N GLU A 948 " --> pdb=" O CYS A 945 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 951 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 955 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 976 removed outlier: 4.035A pdb=" N VAL A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1010 through 1022 Processing helix chain 'A' and resid 1032 through 1047 removed outlier: 4.137A pdb=" N GLU A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1055 No H-bonds generated for 'chain 'A' and resid 1052 through 1055' Processing helix chain 'A' and resid 1061 through 1070 Processing helix chain 'A' and resid 1074 through 1083 Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 4.144A pdb=" N HIS A1096 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP A1097 " --> pdb=" O LYS A1094 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP A1098 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1099 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1130 Processing helix chain 'A' and resid 1135 through 1145 removed outlier: 3.851A pdb=" N ILE A1145 " --> pdb=" O HIS A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.508A pdb=" N LEU A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1200 removed outlier: 4.217A pdb=" N LEU A1188 " --> pdb=" O GLU A1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Proline residue: A1191 - end of helix removed outlier: 4.895A pdb=" N ASN A1200 " --> pdb=" O THR A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1216 through 1234 removed outlier: 3.720A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A1226 " --> pdb=" O GLU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1247 Processing helix chain 'A' and resid 1251 through 1257 Processing helix chain 'A' and resid 1259 through 1268 Processing helix chain 'A' and resid 1283 through 1287 Processing helix chain 'A' and resid 1295 through 1301 Processing helix chain 'A' and resid 1303 through 1313 removed outlier: 3.621A pdb=" N ILE A1313 " --> pdb=" O THR A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1333 through 1343 Processing helix chain 'A' and resid 1360 through 1371 Proline residue: A1364 - end of helix Processing helix chain 'A' and resid 1384 through 1397 Processing helix chain 'A' and resid 1406 through 1421 Processing helix chain 'A' and resid 1429 through 1442 removed outlier: 3.647A pdb=" N SER A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1466 removed outlier: 3.616A pdb=" N GLY A1453 " --> pdb=" O ASP A1449 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A1463 " --> pdb=" O ILE A1459 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR A1465 " --> pdb=" O ARG A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1489 removed outlier: 3.624A pdb=" N GLY A1475 " --> pdb=" O SER A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1521 removed outlier: 3.923A pdb=" N LYS A1502 " --> pdb=" O GLU A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1545 removed outlier: 3.758A pdb=" N HIS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1569 Processing helix chain 'A' and resid 1578 through 1588 Processing helix chain 'A' and resid 1606 through 1619 removed outlier: 5.078A pdb=" N ALA A1614 " --> pdb=" O ILE A1610 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL A1615 " --> pdb=" O LYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1644 Processing helix chain 'A' and resid 1649 through 1651 No H-bonds generated for 'chain 'A' and resid 1649 through 1651' Processing helix chain 'A' and resid 1657 through 1663 Processing helix chain 'A' and resid 1670 through 1683 removed outlier: 3.777A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A1682 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A1683 " --> pdb=" O LYS A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1706 Processing helix chain 'A' and resid 1710 through 1719 removed outlier: 3.574A pdb=" N GLU A1718 " --> pdb=" O SER A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1726 Processing helix chain 'A' and resid 1762 through 1773 removed outlier: 3.849A pdb=" N SER A1773 " --> pdb=" O ARG A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1781 No H-bonds generated for 'chain 'A' and resid 1778 through 1781' Processing helix chain 'A' and resid 1784 through 1787 No H-bonds generated for 'chain 'A' and resid 1784 through 1787' Processing helix chain 'A' and resid 1793 through 1810 Proline residue: A1799 - end of helix removed outlier: 3.657A pdb=" N LEU A1810 " --> pdb=" O LEU A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1827 removed outlier: 4.096A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1851 removed outlier: 3.759A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A1851 " --> pdb=" O LEU A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1862 No H-bonds generated for 'chain 'A' and resid 1860 through 1862' Processing helix chain 'A' and resid 1871 through 1880 Processing helix chain 'A' and resid 1884 through 1898 Processing helix chain 'A' and resid 1916 through 1923 removed outlier: 3.720A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1932 Processing helix chain 'A' and resid 1939 through 1948 Processing helix chain 'A' and resid 1953 through 1968 removed outlier: 3.799A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1988 removed outlier: 3.807A pdb=" N ARG A1975 " --> pdb=" O LEU A1972 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A1988 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2000 removed outlier: 3.624A pdb=" N SER A2000 " --> pdb=" O SER A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2009 through 2021 removed outlier: 3.955A pdb=" N PHE A2015 " --> pdb=" O LEU A2011 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A2017 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A2018 " --> pdb=" O THR A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2047 Processing helix chain 'A' and resid 2052 through 2071 Processing helix chain 'A' and resid 2077 through 2098 removed outlier: 3.628A pdb=" N ASN A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2121 removed outlier: 4.976A pdb=" N SER A2121 " --> pdb=" O LYS A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2143 Processing helix chain 'A' and resid 2154 through 2174 Processing helix chain 'A' and resid 2178 through 2196 removed outlier: 3.817A pdb=" N LEU A2191 " --> pdb=" O ALA A2187 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A2192 " --> pdb=" O LEU A2188 " (cutoff:3.500A) Proline residue: A2193 - end of helix Processing helix chain 'A' and resid 2203 through 2217 Processing helix chain 'A' and resid 2220 through 2232 Processing helix chain 'A' and resid 2245 through 2258 Processing helix chain 'A' and resid 2264 through 2270 removed outlier: 3.918A pdb=" N GLN A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A2269 " --> pdb=" O ASP A2265 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2278 Processing helix chain 'A' and resid 2286 through 2303 Processing helix chain 'A' and resid 2306 through 2329 Processing helix chain 'A' and resid 2349 through 2385 Processing helix chain 'A' and resid 2394 through 2404 Processing helix chain 'A' and resid 2409 through 2421 removed outlier: 5.239A pdb=" N ASN A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS A2421 " --> pdb=" O LYS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2426 No H-bonds generated for 'chain 'A' and resid 2424 through 2426' Processing helix chain 'A' and resid 2431 through 2434 No H-bonds generated for 'chain 'A' and resid 2431 through 2434' Processing helix chain 'A' and resid 2444 through 2459 removed outlier: 3.685A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2472 removed outlier: 5.841A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2499 removed outlier: 3.913A pdb=" N LYS A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2541 through 2552 Processing helix chain 'A' and resid 2616 through 2635 removed outlier: 3.930A pdb=" N LYS A2634 " --> pdb=" O SER A2630 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A2635 " --> pdb=" O GLU A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'A' and resid 2670 through 2681 Proline residue: A2676 - end of helix removed outlier: 3.933A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2688 through 2699 removed outlier: 3.880A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A2699 " --> pdb=" O ILE A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2716 removed outlier: 3.903A pdb=" N ARG A2716 " --> pdb=" O ARG A2712 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2728 removed outlier: 3.792A pdb=" N PHE A2725 " --> pdb=" O ARG A2722 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A2727 " --> pdb=" O PHE A2724 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A2728 " --> pdb=" O PHE A2725 " (cutoff:3.500A) Processing helix chain 'A' and resid 2732 through 2755 Processing helix chain 'A' and resid 2763 through 2765 No H-bonds generated for 'chain 'A' and resid 2763 through 2765' Processing helix chain 'A' and resid 2786 through 2789 removed outlier: 3.675A pdb=" N VAL A2789 " --> pdb=" O MET A2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2786 through 2789' Processing helix chain 'A' and resid 2802 through 2808 removed outlier: 4.500A pdb=" N MET A2808 " --> pdb=" O ILE A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2828 Processing helix chain 'A' and resid 2832 through 2843 Processing helix chain 'A' and resid 2854 through 2860 Processing helix chain 'A' and resid 2898 through 2909 Processing helix chain 'A' and resid 2916 through 2927 Processing helix chain 'A' and resid 2930 through 2935 removed outlier: 4.433A pdb=" N VAL A2935 " --> pdb=" O SER A2931 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 26 through 39 WARNING: missing atoms! Processing helix chain 'B' and resid 56 through 72 Processing helix chain 'B' and resid 86 through 102 Proline residue: B 95 - end of helix Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.990A pdb=" N ALA B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 178 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.859A pdb=" N GLN B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 359 Processing helix chain 'B' and resid 399 through 415 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 458 through 474 removed outlier: 4.196A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Proline residue: B 469 - end of helix removed outlier: 4.137A pdb=" N HIS B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 Processing helix chain 'B' and resid 498 through 513 removed outlier: 4.494A pdb=" N ILE B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 534 removed outlier: 6.145A pdb=" N SER B 524 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 556 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 585 through 601 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 666 through 675 Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 716 through 742 Proline residue: B 730 - end of helix removed outlier: 3.835A pdb=" N TRP B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 770 Processing helix chain 'B' and resid 784 through 802 Processing helix chain 'B' and resid 810 through 821 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 838 through 857 Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 900 through 920 Processing helix chain 'B' and resid 929 through 935 Processing helix chain 'B' and resid 945 through 955 removed outlier: 4.346A pdb=" N GLU B 948 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 951 " --> pdb=" O GLU B 948 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 955 " --> pdb=" O GLU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 removed outlier: 4.035A pdb=" N VAL B 976 " --> pdb=" O ALA B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 997 Processing helix chain 'B' and resid 999 through 1002 No H-bonds generated for 'chain 'B' and resid 999 through 1002' Processing helix chain 'B' and resid 1010 through 1022 Processing helix chain 'B' and resid 1032 through 1047 removed outlier: 4.137A pdb=" N GLU B1047 " --> pdb=" O LEU B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1055 No H-bonds generated for 'chain 'B' and resid 1052 through 1055' Processing helix chain 'B' and resid 1061 through 1070 Processing helix chain 'B' and resid 1074 through 1083 Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'B' and resid 1093 through 1106 removed outlier: 4.144A pdb=" N HIS B1096 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP B1097 " --> pdb=" O LYS B1094 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP B1098 " --> pdb=" O THR B1095 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B1099 " --> pdb=" O HIS B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1130 Processing helix chain 'B' and resid 1135 through 1145 removed outlier: 3.851A pdb=" N ILE B1145 " --> pdb=" O HIS B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1177 removed outlier: 3.508A pdb=" N LEU B1177 " --> pdb=" O ILE B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1200 removed outlier: 4.217A pdb=" N LEU B1188 " --> pdb=" O GLU B1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B1189 " --> pdb=" O LEU B1185 " (cutoff:3.500A) Proline residue: B1191 - end of helix removed outlier: 4.895A pdb=" N ASN B1200 " --> pdb=" O THR B1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1205 No H-bonds generated for 'chain 'B' and resid 1203 through 1205' Processing helix chain 'B' and resid 1216 through 1234 removed outlier: 3.720A pdb=" N ARG B1221 " --> pdb=" O LEU B1217 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B1222 " --> pdb=" O ASP B1218 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR B1225 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU B1226 " --> pdb=" O GLU B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1247 Processing helix chain 'B' and resid 1251 through 1257 Processing helix chain 'B' and resid 1259 through 1268 Processing helix chain 'B' and resid 1283 through 1287 Processing helix chain 'B' and resid 1295 through 1301 Processing helix chain 'B' and resid 1303 through 1313 removed outlier: 3.621A pdb=" N ILE B1313 " --> pdb=" O THR B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1319 through 1323 Processing helix chain 'B' and resid 1333 through 1343 Processing helix chain 'B' and resid 1360 through 1371 Proline residue: B1364 - end of helix Processing helix chain 'B' and resid 1384 through 1397 Processing helix chain 'B' and resid 1406 through 1421 Processing helix chain 'B' and resid 1429 through 1442 removed outlier: 3.647A pdb=" N SER B1437 " --> pdb=" O MET B1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 1449 through 1466 removed outlier: 3.616A pdb=" N GLY B1453 " --> pdb=" O ASP B1449 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B1463 " --> pdb=" O ILE B1459 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B1464 " --> pdb=" O LYS B1460 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR B1465 " --> pdb=" O ARG B1461 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1489 removed outlier: 3.624A pdb=" N GLY B1475 " --> pdb=" O SER B1471 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1521 removed outlier: 3.923A pdb=" N LYS B1502 " --> pdb=" O GLU B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1530 through 1545 removed outlier: 3.758A pdb=" N HIS B1545 " --> pdb=" O GLU B1541 " (cutoff:3.500A) Processing helix chain 'B' and resid 1557 through 1569 Processing helix chain 'B' and resid 1578 through 1588 Processing helix chain 'B' and resid 1606 through 1619 removed outlier: 5.078A pdb=" N ALA B1614 " --> pdb=" O ILE B1610 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL B1615 " --> pdb=" O LYS B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1627 through 1644 Processing helix chain 'B' and resid 1649 through 1651 No H-bonds generated for 'chain 'B' and resid 1649 through 1651' Processing helix chain 'B' and resid 1657 through 1663 Processing helix chain 'B' and resid 1670 through 1683 removed outlier: 3.777A pdb=" N LEU B1681 " --> pdb=" O LEU B1677 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B1682 " --> pdb=" O ILE B1678 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1687 through 1706 Processing helix chain 'B' and resid 1710 through 1719 removed outlier: 3.574A pdb=" N GLU B1718 " --> pdb=" O SER B1714 " (cutoff:3.500A) Processing helix chain 'B' and resid 1722 through 1726 Processing helix chain 'B' and resid 1762 through 1773 removed outlier: 3.849A pdb=" N SER B1773 " --> pdb=" O ARG B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1778 through 1781 No H-bonds generated for 'chain 'B' and resid 1778 through 1781' Processing helix chain 'B' and resid 1784 through 1787 No H-bonds generated for 'chain 'B' and resid 1784 through 1787' Processing helix chain 'B' and resid 1793 through 1810 Proline residue: B1799 - end of helix removed outlier: 3.657A pdb=" N LEU B1810 " --> pdb=" O LEU B1806 " (cutoff:3.500A) Processing helix chain 'B' and resid 1815 through 1827 removed outlier: 4.096A pdb=" N GLN B1825 " --> pdb=" O SER B1821 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1836 through 1851 removed outlier: 3.759A pdb=" N LEU B1841 " --> pdb=" O GLU B1837 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B1851 " --> pdb=" O LEU B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1860 through 1862 No H-bonds generated for 'chain 'B' and resid 1860 through 1862' Processing helix chain 'B' and resid 1871 through 1880 Processing helix chain 'B' and resid 1884 through 1898 Processing helix chain 'B' and resid 1916 through 1923 removed outlier: 3.720A pdb=" N ASN B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1932 Processing helix chain 'B' and resid 1939 through 1948 Processing helix chain 'B' and resid 1953 through 1968 removed outlier: 3.799A pdb=" N PHE B1958 " --> pdb=" O LYS B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1972 through 1988 removed outlier: 3.807A pdb=" N ARG B1975 " --> pdb=" O LEU B1972 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B1988 " --> pdb=" O LEU B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1991 through 2000 removed outlier: 3.624A pdb=" N SER B2000 " --> pdb=" O SER B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2009 through 2021 removed outlier: 3.955A pdb=" N PHE B2015 " --> pdb=" O LEU B2011 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B2017 " --> pdb=" O ALA B2013 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B2018 " --> pdb=" O THR B2014 " (cutoff:3.500A) Processing helix chain 'B' and resid 2035 through 2047 Processing helix chain 'B' and resid 2052 through 2071 Processing helix chain 'B' and resid 2077 through 2098 removed outlier: 3.628A pdb=" N ASN B2098 " --> pdb=" O ASP B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2121 removed outlier: 4.976A pdb=" N SER B2121 " --> pdb=" O LYS B2117 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2143 Processing helix chain 'B' and resid 2154 through 2174 Processing helix chain 'B' and resid 2178 through 2196 removed outlier: 3.817A pdb=" N LEU B2191 " --> pdb=" O ALA B2187 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B2192 " --> pdb=" O LEU B2188 " (cutoff:3.500A) Proline residue: B2193 - end of helix Processing helix chain 'B' and resid 2203 through 2217 Processing helix chain 'B' and resid 2220 through 2232 Processing helix chain 'B' and resid 2245 through 2258 Processing helix chain 'B' and resid 2264 through 2270 removed outlier: 3.918A pdb=" N GLN B2268 " --> pdb=" O PRO B2264 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B2269 " --> pdb=" O ASP B2265 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2278 Processing helix chain 'B' and resid 2286 through 2303 Processing helix chain 'B' and resid 2306 through 2329 Processing helix chain 'B' and resid 2349 through 2385 Processing helix chain 'B' and resid 2394 through 2404 Processing helix chain 'B' and resid 2409 through 2421 removed outlier: 5.239A pdb=" N ASN B2420 " --> pdb=" O LYS B2416 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS B2421 " --> pdb=" O LYS B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2424 through 2426 No H-bonds generated for 'chain 'B' and resid 2424 through 2426' Processing helix chain 'B' and resid 2431 through 2434 No H-bonds generated for 'chain 'B' and resid 2431 through 2434' Processing helix chain 'B' and resid 2444 through 2459 removed outlier: 3.685A pdb=" N ASP B2451 " --> pdb=" O LYS B2447 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2472 removed outlier: 5.841A pdb=" N TYR B2466 " --> pdb=" O TYR B2462 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2483 through 2499 removed outlier: 3.913A pdb=" N LYS B2499 " --> pdb=" O LYS B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2507 through 2522 Processing helix chain 'B' and resid 2541 through 2552 Processing helix chain 'B' and resid 2616 through 2635 removed outlier: 3.930A pdb=" N LYS B2634 " --> pdb=" O SER B2630 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU B2635 " --> pdb=" O GLU B2631 " (cutoff:3.500A) Processing helix chain 'B' and resid 2637 through 2641 Processing helix chain 'B' and resid 2670 through 2681 Proline residue: B2676 - end of helix removed outlier: 3.933A pdb=" N GLU B2679 " --> pdb=" O MET B2675 " (cutoff:3.500A) Processing helix chain 'B' and resid 2688 through 2699 removed outlier: 3.880A pdb=" N ALA B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B2699 " --> pdb=" O ILE B2695 " (cutoff:3.500A) Processing helix chain 'B' and resid 2703 through 2716 removed outlier: 3.903A pdb=" N ARG B2716 " --> pdb=" O ARG B2712 " (cutoff:3.500A) Processing helix chain 'B' and resid 2721 through 2728 removed outlier: 3.792A pdb=" N PHE B2725 " --> pdb=" O ARG B2722 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B2727 " --> pdb=" O PHE B2724 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B2728 " --> pdb=" O PHE B2725 " (cutoff:3.500A) Processing helix chain 'B' and resid 2732 through 2755 Processing helix chain 'B' and resid 2763 through 2765 No H-bonds generated for 'chain 'B' and resid 2763 through 2765' Processing helix chain 'B' and resid 2786 through 2789 removed outlier: 3.675A pdb=" N VAL B2789 " --> pdb=" O MET B2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2786 through 2789' Processing helix chain 'B' and resid 2802 through 2808 removed outlier: 4.500A pdb=" N MET B2808 " --> pdb=" O ILE B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2816 through 2828 Processing helix chain 'B' and resid 2832 through 2843 Processing helix chain 'B' and resid 2854 through 2860 Processing helix chain 'B' and resid 2898 through 2909 Processing helix chain 'B' and resid 2916 through 2927 Processing helix chain 'B' and resid 2930 through 2935 removed outlier: 4.433A pdb=" N VAL B2935 " --> pdb=" O SER B2931 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2534 through 2536 Processing sheet with id= B, first strand: chain 'A' and resid 2651 through 2655 removed outlier: 6.705A pdb=" N SER A2658 " --> pdb=" O LEU A2654 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2667 through 2669 Processing sheet with id= D, first strand: chain 'B' and resid 2534 through 2536 Processing sheet with id= E, first strand: chain 'B' and resid 2651 through 2655 removed outlier: 6.705A pdb=" N SER B2658 " --> pdb=" O LEU B2654 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B2593 " --> pdb=" O VAL B2609 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 2667 through 2669 2232 hydrogen bonds defined for protein. 6432 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: 18.74 Time building geometry restraints manager: 16.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 14476 1.36 - 1.51: 13860 1.51 - 1.65: 14044 1.65 - 1.80: 260 1.80 - 1.95: 38 Bond restraints: 42678 Sorted by residual: bond pdb=" C ILE B1084 " pdb=" N PRO B1085 " ideal model delta sigma weight residual 1.337 1.364 -0.028 9.80e-03 1.04e+04 8.01e+00 bond pdb=" C ILE A1084 " pdb=" N PRO A1085 " ideal model delta sigma weight residual 1.337 1.364 -0.028 9.80e-03 1.04e+04 8.01e+00 bond pdb=" CG LEU A1917 " pdb=" CD2 LEU A1917 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.37e+00 bond pdb=" CG LEU B1917 " pdb=" CD2 LEU B1917 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.37e+00 bond pdb=" CB THR B2740 " pdb=" CG2 THR B2740 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 ... (remaining 42673 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.08: 746 105.08 - 112.40: 22682 112.40 - 119.71: 14884 119.71 - 127.02: 18978 127.02 - 134.33: 530 Bond angle restraints: 57820 Sorted by residual: angle pdb=" N SER B2007 " pdb=" CA SER B2007 " pdb=" CB SER B2007 " ideal model delta sigma weight residual 110.49 98.95 11.54 1.69e+00 3.50e-01 4.66e+01 angle pdb=" N SER A2007 " pdb=" CA SER A2007 " pdb=" CB SER A2007 " ideal model delta sigma weight residual 110.49 98.95 11.54 1.69e+00 3.50e-01 4.66e+01 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 115.64 107.79 7.85 1.46e+00 4.69e-01 2.89e+01 angle pdb=" N GLY A 162 " pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 115.64 107.79 7.85 1.46e+00 4.69e-01 2.89e+01 angle pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta sigma weight residual 121.54 128.56 -7.02 1.91e+00 2.74e-01 1.35e+01 ... (remaining 57815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 23372 17.93 - 35.86: 2024 35.86 - 53.79: 490 53.79 - 71.72: 108 71.72 - 89.65: 36 Dihedral angle restraints: 26030 sinusoidal: 10516 harmonic: 15514 Sorted by residual: dihedral pdb=" CA GLY B2006 " pdb=" C GLY B2006 " pdb=" N SER B2007 " pdb=" CA SER B2007 " ideal model delta harmonic sigma weight residual -180.00 -144.04 -35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA GLY A2006 " pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta harmonic sigma weight residual -180.00 -144.04 -35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA MET B 259 " pdb=" C MET B 259 " pdb=" N LYS B 260 " pdb=" CA LYS B 260 " ideal model delta harmonic sigma weight residual -180.00 -147.24 -32.76 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 26027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3794 0.039 - 0.078: 2160 0.078 - 0.117: 536 0.117 - 0.156: 130 0.156 - 0.195: 10 Chirality restraints: 6630 Sorted by residual: chirality pdb=" CA PRO A 666 " pdb=" N PRO A 666 " pdb=" C PRO A 666 " pdb=" CB PRO A 666 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA PRO B 666 " pdb=" N PRO B 666 " pdb=" C PRO B 666 " pdb=" CB PRO B 666 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CB ILE B 233 " pdb=" CA ILE B 233 " pdb=" CG1 ILE B 233 " pdb=" CG2 ILE B 233 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 6627 not shown) Planarity restraints: 7372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B1854 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO B1855 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B1855 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B1855 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1854 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO A1855 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1855 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1855 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 383 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 384 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.040 5.00e-02 4.00e+02 ... (remaining 7369 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 4 1.80 - 2.58: 370 2.58 - 3.35: 53914 3.35 - 4.13: 95496 4.13 - 4.90: 187039 Nonbonded interactions: 336823 Sorted by model distance: nonbonded pdb=" CG1 ILE A 577 " pdb=" OE2 GLU B 726 " model vdw 1.031 3.440 nonbonded pdb=" OE2 GLU A 726 " pdb=" CG1 ILE B 577 " model vdw 1.031 3.440 nonbonded pdb=" OD2 ASP A2190 " pdb=" OG SER B1965 " model vdw 1.792 2.440 nonbonded pdb=" OG SER A1965 " pdb=" OD2 ASP B2190 " model vdw 1.792 2.440 nonbonded pdb=" OD1 ASP B2012 " pdb=" OG SER B2034 " model vdw 1.871 2.440 ... (remaining 336818 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' } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.210 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 107.650 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.090 42678 Z= 0.695 Angle : 0.816 14.205 57820 Z= 0.442 Chirality : 0.048 0.195 6630 Planarity : 0.005 0.078 7372 Dihedral : 14.877 89.654 15896 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.47 % Favored : 92.45 % Rotamer: Outliers : 5.39 % Allowed : 10.35 % Favored : 84.26 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.09 (0.10), residues: 5192 helix: -1.48 (0.07), residues: 3674 sheet: -0.93 (0.64), residues: 62 loop : -3.27 (0.13), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A2735 HIS 0.007 0.001 HIS A1512 PHE 0.020 0.003 PHE B1741 TYR 0.026 0.003 TYR A1295 ARG 0.005 0.001 ARG B2788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1147 time to evaluate : 4.952 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR B 27 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 325 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 362 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5392 (pm20) REVERT: A 607 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8513 (mm-40) REVERT: A 762 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 1002 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7501 (p-90) REVERT: A 1162 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.6911 (t) REVERT: A 1300 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5651 (m-70) REVERT: A 1376 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.3884 (m-80) REVERT: A 1589 CYS cc_start: 0.7993 (m) cc_final: 0.7770 (m) REVERT: A 1925 ASP cc_start: 0.7783 (t0) cc_final: 0.7108 (t0) REVERT: A 2119 MET cc_start: 0.8947 (mtt) cc_final: 0.8607 (mtt) REVERT: A 2564 VAL cc_start: 0.9175 (t) cc_final: 0.8944 (m) REVERT: B 325 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 362 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5391 (pm20) REVERT: B 502 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8305 (t) REVERT: B 607 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8524 (mm-40) REVERT: B 762 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 1002 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7510 (p-90) REVERT: B 1162 SER cc_start: 0.7649 (OUTLIER) cc_final: 0.6905 (t) REVERT: B 1300 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5647 (m-70) REVERT: B 1376 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.3885 (m-80) REVERT: B 1925 ASP cc_start: 0.7780 (t0) cc_final: 0.7100 (t0) REVERT: B 2119 MET cc_start: 0.8945 (mtt) cc_final: 0.8609 (mtt) REVERT: B 2564 VAL cc_start: 0.9183 (t) cc_final: 0.8950 (m) outliers start: 246 outliers final: 61 residues processed: 1321 average time/residue: 0.6062 time to fit residues: 1254.9120 Evaluate side-chains 600 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 522 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain B residue 1243 LEU Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1410 VAL Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1585 LEU Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 2126 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 444 optimal weight: 0.8980 chunk 398 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 412 optimal weight: 0.0980 chunk 159 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 306 optimal weight: 0.9990 chunk 477 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 612 HIS A 632 HIS A 674 GLN A 824 HIS A 839 HIS A1028 ASN A1062 GLN A1096 HIS A1175 GLN A1399 HIS A1512 HIS A1573 ASN ** A1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1844 ASN A2031 ASN A2065 ASN A2069 HIS A2179 GLN A2239 GLN A2255 GLN A2294 GLN A2354 GLN A2356 GLN A2420 ASN A2446 GLN A2518 HIS A2624 GLN A2641 GLN A2678 HIS A2754 HIS A2849 GLN A2862 ASN A2925 ASN B 235 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 612 HIS B 632 HIS B 674 GLN B1000 ASN B1028 ASN B1062 GLN B1096 HIS B1175 GLN B1399 HIS B1512 HIS B1573 ASN ** B1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1844 ASN B2031 ASN B2065 ASN B2069 HIS B2179 GLN B2239 GLN B2255 GLN B2294 GLN B2354 GLN B2356 GLN B2360 GLN B2361 GLN B2446 GLN B2518 HIS B2624 GLN B2641 GLN B2678 HIS B2754 HIS B2849 GLN B2862 ASN B2925 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42678 Z= 0.196 Angle : 0.604 11.297 57820 Z= 0.304 Chirality : 0.040 0.274 6630 Planarity : 0.005 0.061 7372 Dihedral : 7.391 79.559 5883 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.25 % Allowed : 16.02 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5192 helix: 0.23 (0.08), residues: 3694 sheet: -0.75 (0.66), residues: 66 loop : -2.75 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2118 HIS 0.015 0.001 HIS B1399 PHE 0.023 0.001 PHE A 64 TYR 0.019 0.001 TYR A1195 ARG 0.008 0.000 ARG A1412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 604 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.8500 (p) cc_final: 0.8273 (p) REVERT: A 325 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7303 (t80) REVERT: A 362 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: A 476 LYS cc_start: 0.5728 (tptm) cc_final: 0.5499 (tptm) REVERT: A 591 MET cc_start: 0.8222 (mmp) cc_final: 0.7923 (mmm) REVERT: A 674 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: A 762 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8279 (t) REVERT: A 771 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 1002 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.7188 (p-90) REVERT: A 1030 MET cc_start: 0.7234 (mmm) cc_final: 0.6978 (mtt) REVERT: A 1292 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6233 (tppt) REVERT: A 1300 HIS cc_start: 0.6090 (OUTLIER) cc_final: 0.5682 (m-70) REVERT: A 1376 TYR cc_start: 0.5294 (OUTLIER) cc_final: 0.3669 (m-80) REVERT: A 1589 CYS cc_start: 0.8057 (m) cc_final: 0.7782 (m) REVERT: A 1854 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 1925 ASP cc_start: 0.7459 (t0) cc_final: 0.7129 (t0) REVERT: A 1964 ASP cc_start: 0.8089 (m-30) cc_final: 0.7743 (m-30) REVERT: A 2119 MET cc_start: 0.8645 (mtt) cc_final: 0.8434 (mtt) REVERT: A 2749 ILE cc_start: 0.8928 (tp) cc_final: 0.8661 (tp) REVERT: A 2758 LEU cc_start: 0.9059 (tp) cc_final: 0.8850 (tp) REVERT: B 275 VAL cc_start: 0.8497 (p) cc_final: 0.8272 (p) REVERT: B 325 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7319 (t80) REVERT: B 362 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5818 (pm20) REVERT: B 476 LYS cc_start: 0.5731 (tptm) cc_final: 0.5514 (tptm) REVERT: B 591 MET cc_start: 0.8166 (mmp) cc_final: 0.7862 (mmm) REVERT: B 674 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: B 762 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8282 (t) REVERT: B 771 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8148 (pp) REVERT: B 1002 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7198 (p-90) REVERT: B 1030 MET cc_start: 0.7229 (mmm) cc_final: 0.6968 (mtt) REVERT: B 1292 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6228 (tppt) REVERT: B 1300 HIS cc_start: 0.6095 (OUTLIER) cc_final: 0.5688 (m-70) REVERT: B 1376 TYR cc_start: 0.5302 (OUTLIER) cc_final: 0.3681 (m-80) REVERT: B 1589 CYS cc_start: 0.7886 (m) cc_final: 0.7670 (m) REVERT: B 1854 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7988 (tp) REVERT: B 1925 ASP cc_start: 0.7461 (t0) cc_final: 0.7122 (t0) REVERT: B 1964 ASP cc_start: 0.8075 (m-30) cc_final: 0.7734 (m-30) REVERT: B 2119 MET cc_start: 0.8639 (mtt) cc_final: 0.8434 (mtt) REVERT: B 2749 ILE cc_start: 0.8928 (tp) cc_final: 0.8662 (tp) REVERT: B 2758 LEU cc_start: 0.9060 (tp) cc_final: 0.8850 (tp) outliers start: 194 outliers final: 110 residues processed: 760 average time/residue: 0.5725 time to fit residues: 723.3828 Evaluate side-chains 574 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 444 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2429 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2493 ILE Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2929 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1292 LYS Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1410 VAL Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2429 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2493 ILE Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2505 SER Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2792 VAL Chi-restraints excluded: chain B residue 2805 VAL Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2929 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 265 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 397 optimal weight: 5.9990 chunk 325 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 478 optimal weight: 0.9980 chunk 516 optimal weight: 0.8980 chunk 426 optimal weight: 0.0570 chunk 474 optimal weight: 0.5980 chunk 163 optimal weight: 0.0570 chunk 383 optimal weight: 6.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 407 ASN A 674 GLN A 803 ASN A1000 ASN A1106 HIS ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2239 GLN A2501 ASN B 368 GLN B 407 ASN B 674 GLN B 803 ASN B 839 HIS B 934 GLN B1106 HIS ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2239 GLN B2501 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 42678 Z= 0.157 Angle : 0.541 9.626 57820 Z= 0.270 Chirality : 0.038 0.263 6630 Planarity : 0.004 0.051 7372 Dihedral : 6.721 81.483 5844 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.57 % Allowed : 17.43 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 5192 helix: 0.98 (0.09), residues: 3702 sheet: -0.39 (0.64), residues: 76 loop : -2.47 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1002 HIS 0.005 0.001 HIS B1106 PHE 0.026 0.001 PHE B1259 TYR 0.015 0.001 TYR B1195 ARG 0.006 0.000 ARG B1412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 501 time to evaluate : 4.463 Fit side-chains revert: symmetry clash REVERT: A 328 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7434 (ttp-170) REVERT: A 771 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 1002 TRP cc_start: 0.8102 (OUTLIER) cc_final: 0.7178 (p-90) REVERT: A 1292 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.6099 (tppt) REVERT: A 1300 HIS cc_start: 0.5993 (OUTLIER) cc_final: 0.5599 (m170) REVERT: A 1376 TYR cc_start: 0.5171 (OUTLIER) cc_final: 0.3638 (m-80) REVERT: A 1406 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6572 (t70) REVERT: A 1589 CYS cc_start: 0.7966 (m) cc_final: 0.7675 (m) REVERT: A 1854 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7838 (tp) REVERT: A 1925 ASP cc_start: 0.7382 (t0) cc_final: 0.7129 (t0) REVERT: A 2119 MET cc_start: 0.8661 (mtt) cc_final: 0.8435 (mtt) REVERT: A 2758 LEU cc_start: 0.8999 (tp) cc_final: 0.8780 (tp) REVERT: A 2925 ASN cc_start: 0.8328 (m-40) cc_final: 0.7911 (m110) REVERT: B 591 MET cc_start: 0.8157 (mmp) cc_final: 0.7936 (tpp) REVERT: B 771 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8378 (pp) REVERT: B 1002 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7183 (p-90) REVERT: B 1292 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.6095 (tppt) REVERT: B 1300 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.5599 (m170) REVERT: B 1376 TYR cc_start: 0.5175 (OUTLIER) cc_final: 0.3637 (m-80) REVERT: B 1406 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6560 (t70) REVERT: B 1854 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7850 (tp) REVERT: B 1925 ASP cc_start: 0.7381 (t0) cc_final: 0.7121 (t0) REVERT: B 2119 MET cc_start: 0.8657 (mtt) cc_final: 0.8436 (mtt) REVERT: B 2758 LEU cc_start: 0.8994 (tp) cc_final: 0.8771 (tp) REVERT: B 2925 ASN cc_start: 0.8317 (m-40) cc_final: 0.7895 (m110) outliers start: 163 outliers final: 93 residues processed: 622 average time/residue: 0.5715 time to fit residues: 595.1988 Evaluate side-chains 548 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 440 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2929 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1145 ILE Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1292 LYS Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2929 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 472 optimal weight: 9.9990 chunk 359 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 480 optimal weight: 5.9990 chunk 508 optimal weight: 1.9990 chunk 250 optimal weight: 0.2980 chunk 455 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42678 Z= 0.201 Angle : 0.540 9.359 57820 Z= 0.268 Chirality : 0.039 0.264 6630 Planarity : 0.004 0.046 7372 Dihedral : 6.489 84.246 5822 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.27 % Allowed : 17.93 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 5192 helix: 1.32 (0.09), residues: 3712 sheet: -0.36 (0.65), residues: 76 loop : -2.24 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1002 HIS 0.007 0.001 HIS B 120 PHE 0.041 0.001 PHE A2546 TYR 0.016 0.001 TYR B2517 ARG 0.009 0.000 ARG A1130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 455 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 LEU cc_start: 0.7421 (tp) cc_final: 0.7155 (tt) REVERT: A 388 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (tp) REVERT: A 771 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8406 (pp) REVERT: A 1119 PHE cc_start: 0.8927 (t80) cc_final: 0.8661 (t80) REVERT: A 1193 LEU cc_start: 0.8340 (mt) cc_final: 0.8081 (mt) REVERT: A 1300 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.5564 (m170) REVERT: A 1376 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.3441 (m-80) REVERT: A 1406 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6468 (t70) REVERT: A 1589 CYS cc_start: 0.8086 (m) cc_final: 0.7817 (m) REVERT: A 1854 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7797 (tp) REVERT: A 1925 ASP cc_start: 0.7358 (t0) cc_final: 0.7091 (t0) REVERT: A 2925 ASN cc_start: 0.8408 (m-40) cc_final: 0.7977 (m110) REVERT: B 298 LEU cc_start: 0.7364 (tp) cc_final: 0.7134 (tt) REVERT: B 388 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8208 (tp) REVERT: B 771 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 1119 PHE cc_start: 0.8926 (t80) cc_final: 0.8664 (t80) REVERT: B 1193 LEU cc_start: 0.8335 (mt) cc_final: 0.8070 (mt) REVERT: B 1300 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.5568 (m170) REVERT: B 1376 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.3449 (m-80) REVERT: B 1406 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6462 (t70) REVERT: B 1854 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7808 (tp) REVERT: B 1925 ASP cc_start: 0.7357 (t0) cc_final: 0.7081 (t0) REVERT: B 2925 ASN cc_start: 0.8398 (m-40) cc_final: 0.7963 (m110) outliers start: 195 outliers final: 128 residues processed: 595 average time/residue: 0.5175 time to fit residues: 516.0870 Evaluate side-chains 537 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 397 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2156 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2429 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2746 THR Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1047 GLU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1090 LEU Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1783 LEU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2156 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2429 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2746 THR Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 423 optimal weight: 0.0770 chunk 288 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 378 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 433 optimal weight: 2.9990 chunk 351 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 456 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42678 Z= 0.218 Angle : 0.546 10.519 57820 Z= 0.271 Chirality : 0.039 0.254 6630 Planarity : 0.004 0.043 7372 Dihedral : 6.073 85.283 5818 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.49 % Allowed : 18.52 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.12), residues: 5192 helix: 1.55 (0.09), residues: 3706 sheet: -0.44 (0.67), residues: 66 loop : -2.04 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1002 HIS 0.008 0.001 HIS B 120 PHE 0.031 0.001 PHE B 272 TYR 0.016 0.001 TYR B 145 ARG 0.013 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 444 time to evaluate : 4.841 Fit side-chains REVERT: A 298 LEU cc_start: 0.7482 (tp) cc_final: 0.7235 (tt) REVERT: A 388 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8163 (tp) REVERT: A 755 MET cc_start: 0.7700 (tpp) cc_final: 0.7228 (tpt) REVERT: A 771 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8471 (pp) REVERT: A 1119 PHE cc_start: 0.8899 (t80) cc_final: 0.8622 (t80) REVERT: A 1300 HIS cc_start: 0.5890 (OUTLIER) cc_final: 0.5633 (m90) REVERT: A 1376 TYR cc_start: 0.5134 (OUTLIER) cc_final: 0.3259 (m-80) REVERT: A 1406 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6322 (t70) REVERT: A 1589 CYS cc_start: 0.8151 (m) cc_final: 0.7856 (m) REVERT: A 1964 ASP cc_start: 0.8300 (m-30) cc_final: 0.7890 (m-30) REVERT: A 2546 PHE cc_start: 0.7496 (t80) cc_final: 0.7282 (t80) REVERT: A 2550 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6894 (mmm) REVERT: A 2624 GLN cc_start: 0.7574 (tt0) cc_final: 0.7281 (tt0) REVERT: A 2925 ASN cc_start: 0.8261 (m-40) cc_final: 0.7908 (m-40) REVERT: B 298 LEU cc_start: 0.7492 (tp) cc_final: 0.7227 (tt) REVERT: B 388 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8155 (tp) REVERT: B 755 MET cc_start: 0.7716 (tpp) cc_final: 0.7215 (tpt) REVERT: B 771 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B 1119 PHE cc_start: 0.8897 (t80) cc_final: 0.8620 (t80) REVERT: B 1300 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.5632 (m90) REVERT: B 1376 TYR cc_start: 0.5145 (OUTLIER) cc_final: 0.3273 (m-80) REVERT: B 1406 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6304 (t70) REVERT: B 1964 ASP cc_start: 0.8283 (m-30) cc_final: 0.7877 (m-30) REVERT: B 2546 PHE cc_start: 0.7501 (t80) cc_final: 0.7285 (t80) REVERT: B 2550 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6905 (mmm) REVERT: B 2624 GLN cc_start: 0.7585 (tt0) cc_final: 0.7278 (tt0) REVERT: B 2925 ASN cc_start: 0.8270 (m-40) cc_final: 0.7862 (m110) outliers start: 205 outliers final: 132 residues processed: 600 average time/residue: 0.5097 time to fit residues: 518.3939 Evaluate side-chains 549 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 405 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2746 THR Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1047 GLU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2746 THR Chi-restraints excluded: chain B residue 2792 VAL Chi-restraints excluded: chain B residue 2805 VAL Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 171 optimal weight: 0.7980 chunk 457 optimal weight: 0.0050 chunk 100 optimal weight: 0.5980 chunk 298 optimal weight: 0.1980 chunk 125 optimal weight: 7.9990 chunk 508 optimal weight: 0.8980 chunk 422 optimal weight: 0.9980 chunk 235 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42678 Z= 0.144 Angle : 0.514 9.571 57820 Z= 0.251 Chirality : 0.037 0.278 6630 Planarity : 0.004 0.043 7372 Dihedral : 5.634 84.727 5808 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.27 % Allowed : 20.34 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.25 (0.12), residues: 5192 helix: 1.81 (0.09), residues: 3696 sheet: -0.38 (0.63), residues: 76 loop : -1.82 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1002 HIS 0.011 0.001 HIS B 120 PHE 0.014 0.001 PHE A2546 TYR 0.017 0.001 TYR B 140 ARG 0.004 0.000 ARG B2286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 478 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 LEU cc_start: 0.7532 (tp) cc_final: 0.7322 (tt) REVERT: A 388 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8149 (tp) REVERT: A 753 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.5730 (m) REVERT: A 755 MET cc_start: 0.7689 (tpp) cc_final: 0.7238 (tpt) REVERT: A 771 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 917 ILE cc_start: 0.7951 (mm) cc_final: 0.7682 (mm) REVERT: A 1119 PHE cc_start: 0.8830 (t80) cc_final: 0.8568 (t80) REVERT: A 1300 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.5700 (m90) REVERT: A 1376 TYR cc_start: 0.5073 (OUTLIER) cc_final: 0.3298 (m-80) REVERT: A 1406 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6076 (t70) REVERT: A 1589 CYS cc_start: 0.8037 (m) cc_final: 0.7736 (m) REVERT: A 1964 ASP cc_start: 0.8219 (m-30) cc_final: 0.7833 (m-30) REVERT: A 2056 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7701 (mtt180) REVERT: A 2550 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6777 (mmm) REVERT: A 2615 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7152 (p0) REVERT: A 2624 GLN cc_start: 0.7506 (tt0) cc_final: 0.7204 (tt0) REVERT: A 2925 ASN cc_start: 0.8244 (m-40) cc_final: 0.7865 (m-40) REVERT: B 298 LEU cc_start: 0.7537 (tp) cc_final: 0.7321 (tt) REVERT: B 388 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (tp) REVERT: B 753 VAL cc_start: 0.6141 (OUTLIER) cc_final: 0.5751 (m) REVERT: B 755 MET cc_start: 0.7703 (tpp) cc_final: 0.7237 (tpt) REVERT: B 771 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8460 (pp) REVERT: B 917 ILE cc_start: 0.7940 (mm) cc_final: 0.7672 (mm) REVERT: B 1119 PHE cc_start: 0.8824 (t80) cc_final: 0.8564 (t80) REVERT: B 1300 HIS cc_start: 0.5932 (OUTLIER) cc_final: 0.5702 (m90) REVERT: B 1376 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3303 (m-80) REVERT: B 1406 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6071 (t70) REVERT: B 1964 ASP cc_start: 0.8205 (m-30) cc_final: 0.7820 (m-30) REVERT: B 2056 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7728 (mtt180) REVERT: B 2550 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6791 (mmm) REVERT: B 2615 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7144 (p0) REVERT: B 2624 GLN cc_start: 0.7505 (tt0) cc_final: 0.7193 (tt0) REVERT: B 2925 ASN cc_start: 0.8241 (m-40) cc_final: 0.7866 (m-40) outliers start: 149 outliers final: 108 residues processed: 587 average time/residue: 0.5171 time to fit residues: 511.6787 Evaluate side-chains 550 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 424 time to evaluate : 5.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2156 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2615 ASP Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 2056 ARG Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2156 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2615 ASP Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 490 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 371 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 428 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 506 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42678 Z= 0.179 Angle : 0.532 11.907 57820 Z= 0.260 Chirality : 0.038 0.241 6630 Planarity : 0.004 0.042 7372 Dihedral : 5.498 84.625 5804 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.57 % Allowed : 20.47 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.12), residues: 5192 helix: 1.92 (0.09), residues: 3670 sheet: -0.39 (0.67), residues: 66 loop : -1.71 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1002 HIS 0.012 0.001 HIS B 120 PHE 0.046 0.001 PHE B1259 TYR 0.012 0.001 TYR B 140 ARG 0.004 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 450 time to evaluate : 4.653 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8042 (tp) REVERT: A 753 VAL cc_start: 0.6165 (OUTLIER) cc_final: 0.5772 (m) REVERT: A 917 ILE cc_start: 0.8077 (mm) cc_final: 0.7840 (mm) REVERT: A 1217 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7285 (mm) REVERT: A 1300 HIS cc_start: 0.5872 (OUTLIER) cc_final: 0.5631 (m90) REVERT: A 1376 TYR cc_start: 0.5098 (OUTLIER) cc_final: 0.3491 (m-80) REVERT: A 1589 CYS cc_start: 0.8118 (m) cc_final: 0.7777 (m) REVERT: A 1964 ASP cc_start: 0.8249 (m-30) cc_final: 0.7863 (m-30) REVERT: A 2056 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7960 (mtt90) REVERT: A 2303 LEU cc_start: 0.8954 (mt) cc_final: 0.8693 (tp) REVERT: A 2546 PHE cc_start: 0.7579 (t80) cc_final: 0.7059 (t80) REVERT: A 2550 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6716 (mmm) REVERT: A 2624 GLN cc_start: 0.7565 (tt0) cc_final: 0.7255 (tt0) REVERT: A 2925 ASN cc_start: 0.8369 (m-40) cc_final: 0.7958 (m-40) REVERT: B 388 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 753 VAL cc_start: 0.6191 (OUTLIER) cc_final: 0.5792 (m) REVERT: B 917 ILE cc_start: 0.8064 (mm) cc_final: 0.7839 (mm) REVERT: B 1217 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7283 (mm) REVERT: B 1300 HIS cc_start: 0.5880 (OUTLIER) cc_final: 0.5630 (m90) REVERT: B 1376 TYR cc_start: 0.5103 (OUTLIER) cc_final: 0.3491 (m-80) REVERT: B 1964 ASP cc_start: 0.8232 (m-30) cc_final: 0.7851 (m-30) REVERT: B 2056 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7968 (mtt90) REVERT: B 2303 LEU cc_start: 0.8970 (mt) cc_final: 0.8712 (tp) REVERT: B 2546 PHE cc_start: 0.7598 (t80) cc_final: 0.7074 (t80) REVERT: B 2550 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6737 (mmm) REVERT: B 2624 GLN cc_start: 0.7568 (tt0) cc_final: 0.7246 (tt0) REVERT: B 2925 ASN cc_start: 0.8374 (m-40) cc_final: 0.7953 (m-40) outliers start: 163 outliers final: 121 residues processed: 569 average time/residue: 0.5140 time to fit residues: 495.3933 Evaluate side-chains 558 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 423 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2156 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1047 GLU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2056 ARG Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2156 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 313 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 322 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 250 optimal weight: 0.0370 chunk 47 optimal weight: 0.0770 chunk 398 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 ASN ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42678 Z= 0.149 Angle : 0.519 10.762 57820 Z= 0.252 Chirality : 0.037 0.227 6630 Planarity : 0.004 0.062 7372 Dihedral : 5.330 84.257 5802 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.29 % Allowed : 20.63 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 5192 helix: 2.01 (0.09), residues: 3676 sheet: -0.33 (0.67), residues: 66 loop : -1.60 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.009 0.001 HIS B 235 PHE 0.031 0.001 PHE A1259 TYR 0.011 0.001 TYR B1195 ARG 0.004 0.000 ARG B2286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 465 time to evaluate : 4.717 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 753 VAL cc_start: 0.6170 (OUTLIER) cc_final: 0.5725 (m) REVERT: A 755 MET cc_start: 0.7549 (tpp) cc_final: 0.7247 (tpt) REVERT: A 917 ILE cc_start: 0.8115 (mm) cc_final: 0.7890 (mm) REVERT: A 1217 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7377 (mm) REVERT: A 1300 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5753 (m90) REVERT: A 1376 TYR cc_start: 0.4913 (OUTLIER) cc_final: 0.3479 (m-80) REVERT: A 1589 CYS cc_start: 0.8020 (m) cc_final: 0.7660 (m) REVERT: A 1964 ASP cc_start: 0.8209 (m-30) cc_final: 0.7826 (m-30) REVERT: A 2303 LEU cc_start: 0.8923 (mt) cc_final: 0.8680 (tp) REVERT: A 2615 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7203 (p0) REVERT: A 2624 GLN cc_start: 0.7537 (tt0) cc_final: 0.7215 (tt0) REVERT: A 2631 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 2925 ASN cc_start: 0.8348 (m-40) cc_final: 0.7922 (m110) REVERT: B 233 ILE cc_start: 0.8898 (pt) cc_final: 0.8698 (pt) REVERT: B 388 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 753 VAL cc_start: 0.6180 (OUTLIER) cc_final: 0.5735 (m) REVERT: B 755 MET cc_start: 0.7555 (tpp) cc_final: 0.7239 (tpt) REVERT: B 917 ILE cc_start: 0.8076 (mm) cc_final: 0.7854 (mm) REVERT: B 1217 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7372 (mm) REVERT: B 1300 HIS cc_start: 0.6000 (OUTLIER) cc_final: 0.5754 (m90) REVERT: B 1376 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.3482 (m-80) REVERT: B 1964 ASP cc_start: 0.8197 (m-30) cc_final: 0.7810 (m-30) REVERT: B 2303 LEU cc_start: 0.8935 (mt) cc_final: 0.8690 (tp) REVERT: B 2615 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7194 (p0) REVERT: B 2624 GLN cc_start: 0.7535 (tt0) cc_final: 0.7208 (tt0) REVERT: B 2925 ASN cc_start: 0.8354 (m-40) cc_final: 0.7912 (m110) outliers start: 150 outliers final: 117 residues processed: 571 average time/residue: 0.5202 time to fit residues: 506.5225 Evaluate side-chains 555 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 426 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2156 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2615 ASP Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2156 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2615 ASP Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 461 optimal weight: 1.9990 chunk 485 optimal weight: 0.9990 chunk 443 optimal weight: 0.8980 chunk 472 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 370 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 426 optimal weight: 0.1980 chunk 446 optimal weight: 0.5980 chunk 470 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1256 GLN ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42678 Z= 0.173 Angle : 0.543 11.480 57820 Z= 0.263 Chirality : 0.038 0.282 6630 Planarity : 0.004 0.067 7372 Dihedral : 5.234 84.055 5800 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.16 % Allowed : 20.74 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.12), residues: 5192 helix: 2.05 (0.09), residues: 3668 sheet: -0.23 (0.68), residues: 66 loop : -1.50 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.011 0.001 HIS B 120 PHE 0.036 0.001 PHE B2546 TYR 0.010 0.001 TYR A 140 ARG 0.004 0.000 ARG A2286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 450 time to evaluate : 4.777 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8020 (tp) REVERT: A 753 VAL cc_start: 0.6101 (OUTLIER) cc_final: 0.5696 (m) REVERT: A 917 ILE cc_start: 0.8003 (mm) cc_final: 0.7791 (mm) REVERT: A 1217 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7378 (mm) REVERT: A 1376 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.3271 (m-80) REVERT: A 1589 CYS cc_start: 0.8076 (m) cc_final: 0.7667 (m) REVERT: A 1964 ASP cc_start: 0.8222 (m-30) cc_final: 0.7837 (m-30) REVERT: A 2056 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7989 (mtt90) REVERT: A 2303 LEU cc_start: 0.8917 (mt) cc_final: 0.8679 (tp) REVERT: A 2546 PHE cc_start: 0.7500 (t80) cc_final: 0.7194 (t80) REVERT: A 2550 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6780 (mmm) REVERT: A 2624 GLN cc_start: 0.7564 (tt0) cc_final: 0.7232 (tt0) REVERT: A 2631 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 2925 ASN cc_start: 0.8362 (m-40) cc_final: 0.7939 (m110) REVERT: B 388 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8022 (tp) REVERT: B 753 VAL cc_start: 0.6106 (OUTLIER) cc_final: 0.5706 (m) REVERT: B 917 ILE cc_start: 0.7994 (mm) cc_final: 0.7791 (mm) REVERT: B 1217 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7382 (mm) REVERT: B 1376 TYR cc_start: 0.4930 (OUTLIER) cc_final: 0.3272 (m-80) REVERT: B 1964 ASP cc_start: 0.8204 (m-30) cc_final: 0.7818 (m-30) REVERT: B 2056 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8009 (mtt90) REVERT: B 2303 LEU cc_start: 0.8925 (mt) cc_final: 0.8665 (tp) REVERT: B 2546 PHE cc_start: 0.7527 (t80) cc_final: 0.7205 (t80) REVERT: B 2550 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6801 (mmm) REVERT: B 2624 GLN cc_start: 0.7565 (tt0) cc_final: 0.7218 (tt0) REVERT: B 2631 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 2925 ASN cc_start: 0.8368 (m-40) cc_final: 0.7929 (m110) outliers start: 144 outliers final: 120 residues processed: 554 average time/residue: 0.5056 time to fit residues: 478.0091 Evaluate side-chains 558 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 426 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1074 MET Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1822 GLU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2156 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1728 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1822 GLU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2056 ARG Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2156 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 310 optimal weight: 1.9990 chunk 499 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 347 optimal weight: 7.9990 chunk 524 optimal weight: 0.5980 chunk 482 optimal weight: 0.8980 chunk 417 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 255 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 GLN ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42678 Z= 0.177 Angle : 0.547 14.154 57820 Z= 0.265 Chirality : 0.038 0.332 6630 Planarity : 0.004 0.046 7372 Dihedral : 5.097 83.169 5796 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.02 % Allowed : 21.09 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.12), residues: 5192 helix: 2.10 (0.09), residues: 3648 sheet: -0.32 (0.66), residues: 66 loop : -1.46 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.006 0.001 HIS B 120 PHE 0.041 0.001 PHE A 272 TYR 0.010 0.001 TYR B 145 ARG 0.005 0.000 ARG A 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 450 time to evaluate : 5.064 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 1376 TYR cc_start: 0.4985 (OUTLIER) cc_final: 0.3286 (m-80) REVERT: A 1589 CYS cc_start: 0.8065 (m) cc_final: 0.7663 (m) REVERT: A 1964 ASP cc_start: 0.8242 (m-30) cc_final: 0.7871 (m-30) REVERT: A 2056 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8074 (mtt90) REVERT: A 2303 LEU cc_start: 0.8898 (mt) cc_final: 0.8676 (tp) REVERT: A 2624 GLN cc_start: 0.7567 (tt0) cc_final: 0.7242 (tt0) REVERT: A 2631 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 2925 ASN cc_start: 0.8226 (m-40) cc_final: 0.7832 (m110) REVERT: B 388 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8017 (tp) REVERT: B 1217 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7394 (mm) REVERT: B 1376 TYR cc_start: 0.4991 (OUTLIER) cc_final: 0.3292 (m-80) REVERT: B 1964 ASP cc_start: 0.8227 (m-30) cc_final: 0.7856 (m-30) REVERT: B 2056 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8090 (mtt90) REVERT: B 2303 LEU cc_start: 0.8954 (mt) cc_final: 0.8721 (tp) REVERT: B 2624 GLN cc_start: 0.7566 (tt0) cc_final: 0.7233 (tt0) REVERT: B 2631 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 2925 ASN cc_start: 0.8227 (m-40) cc_final: 0.7822 (m110) outliers start: 138 outliers final: 123 residues processed: 554 average time/residue: 0.5053 time to fit residues: 475.0437 Evaluate side-chains 556 residues out of total 4562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 426 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1822 GLU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2056 ARG Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2156 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1728 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1822 GLU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1915 ASP Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2056 ARG Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2156 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 331 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 384 optimal weight: 0.0270 chunk 61 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 417 optimal weight: 0.0670 chunk 174 optimal weight: 5.9990 chunk 429 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 HIS A1204 GLN A1256 GLN ** A1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B1204 GLN B1256 GLN ** B1573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099387 restraints weight = 74244.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098861 restraints weight = 60446.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099578 restraints weight = 71410.325| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42678 Z= 0.184 Angle : 0.562 14.058 57820 Z= 0.271 Chirality : 0.039 0.329 6630 Planarity : 0.004 0.058 7372 Dihedral : 5.013 82.427 5794 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.07 % Allowed : 20.80 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.12), residues: 5192 helix: 2.13 (0.09), residues: 3652 sheet: -0.36 (0.64), residues: 66 loop : -1.43 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.010 0.001 HIS B 120 PHE 0.038 0.001 PHE A 272 TYR 0.010 0.001 TYR A1017 ARG 0.005 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9824.99 seconds wall clock time: 178 minutes 20.01 seconds (10700.01 seconds total)