Starting phenix.real_space_refine on Sun Mar 24 11:24:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7su3_25439/03_2024/7su3_25439_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7su3_25439/03_2024/7su3_25439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7su3_25439/03_2024/7su3_25439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7su3_25439/03_2024/7su3_25439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7su3_25439/03_2024/7su3_25439_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7su3_25439/03_2024/7su3_25439_updated.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 241 5.16 5 C 26173 2.51 5 N 7007 2.21 5 O 7745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A GLU 1002": "OE1" <-> "OE2" Residue "A ASP 1005": "OD1" <-> "OD2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A GLU 1182": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A ASP 1210": "OD1" <-> "OD2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A PHE 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1258": "OD1" <-> "OD2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A GLU 1285": "OE1" <-> "OE2" Residue "A GLU 1299": "OE1" <-> "OE2" Residue "A GLU 1328": "OE1" <-> "OE2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A ASP 1413": "OD1" <-> "OD2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A GLU 1430": "OE1" <-> "OE2" Residue "A TYR 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1447": "NH1" <-> "NH2" Residue "A ASP 1504": "OD1" <-> "OD2" Residue "A GLU 1570": "OE1" <-> "OE2" Residue "A ASP 1588": "OD1" <-> "OD2" Residue "A ASP 1636": "OD1" <-> "OD2" Residue "A GLU 1640": "OE1" <-> "OE2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A PHE 1746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1775": "OE1" <-> "OE2" Residue "A GLU 1776": "OE1" <-> "OE2" Residue "A ARG 1784": "NH1" <-> "NH2" Residue "A ARG 1788": "NH1" <-> "NH2" Residue "A ASP 1808": "OD1" <-> "OD2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ASP 1846": "OD1" <-> "OD2" Residue "A ASP 1878": "OD1" <-> "OD2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A TYR 1920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1921": "OD1" <-> "OD2" Residue "A GLU 1925": "OE1" <-> "OE2" Residue "A GLU 1930": "OE1" <-> "OE2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A TYR 1945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1983": "OD1" <-> "OD2" Residue "A ARG 1986": "NH1" <-> "NH2" Residue "A ARG 1987": "NH1" <-> "NH2" Residue "A TYR 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1999": "OE1" <-> "OE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A PHE 2157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A GLU 2180": "OE1" <-> "OE2" Residue "A ASP 2284": "OD1" <-> "OD2" Residue "A TYR 2299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A GLU 2314": "OE1" <-> "OE2" Residue "A ARG 2328": "NH1" <-> "NH2" Residue "A PHE 2384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2419": "OD1" <-> "OD2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A GLU 2453": "OE1" <-> "OE2" Residue "A ARG 2485": "NH1" <-> "NH2" Residue "A GLU 2497": "OE1" <-> "OE2" Residue "A ASP 2504": "OD1" <-> "OD2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A GLU 2588": "OE1" <-> "OE2" Residue "A ASP 2592": "OD1" <-> "OD2" Residue "A PHE 2606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2727": "NH1" <-> "NH2" Residue "A ARG 2730": "NH1" <-> "NH2" Residue "A ARG 2731": "NH1" <-> "NH2" Residue "A ASP 2735": "OD1" <-> "OD2" Residue "A GLU 2750": "OE1" <-> "OE2" Residue "A ARG 2753": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A GLU 2819": "OE1" <-> "OE2" Residue "A PHE 2823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2860": "OD1" <-> "OD2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2962": "NH1" <-> "NH2" Residue "A ASP 2964": "OD1" <-> "OD2" Residue "A ASP 3020": "OD1" <-> "OD2" Residue "A GLU 3033": "OE1" <-> "OE2" Residue "A PHE 3035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3118": "OD1" <-> "OD2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A GLU 3195": "OE1" <-> "OE2" Residue "A TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ASP 3308": "OD1" <-> "OD2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A TYR 3334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3353": "OE1" <-> "OE2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A GLU 3361": "OE1" <-> "OE2" Residue "A GLU 3368": "OE1" <-> "OE2" Residue "A ASP 3369": "OD1" <-> "OD2" Residue "A GLU 3387": "OE1" <-> "OE2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3460": "OE1" <-> "OE2" Residue "A ARG 3462": "NH1" <-> "NH2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A GLU 3473": "OE1" <-> "OE2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A TYR 3475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3507": "OD1" <-> "OD2" Residue "A ASP 3509": "OD1" <-> "OD2" Residue "A GLU 3538": "OE1" <-> "OE2" Residue "A GLU 3553": "OE1" <-> "OE2" Residue "A ASP 3570": "OD1" <-> "OD2" Residue "A ASP 3576": "OD1" <-> "OD2" Residue "A GLU 3582": "OE1" <-> "OE2" Residue "A PHE 3585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3587": "OD1" <-> "OD2" Residue "A ASP 3591": "OD1" <-> "OD2" Residue "A GLU 3611": "OE1" <-> "OE2" Residue "A ASP 3619": "OD1" <-> "OD2" Residue "A PHE 3640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3658": "OD1" <-> "OD2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A GLU 3714": "OE1" <-> "OE2" Residue "A GLU 3745": "OE1" <-> "OE2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ASP 3831": "OD1" <-> "OD2" Residue "A ASP 3841": "OD1" <-> "OD2" Residue "A TYR 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A GLU 3866": "OE1" <-> "OE2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A PHE 3904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "A GLU 3957": "OE1" <-> "OE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A ARG 3965": "NH1" <-> "NH2" Residue "A TYR 3981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4017": "OE1" <-> "OE2" Residue "A ARG 4075": "NH1" <-> "NH2" Residue "A ASP 4086": "OD1" <-> "OD2" Residue "A GLU 4095": "OE1" <-> "OE2" Residue "A GLU 4100": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ASP 476": "OD1" <-> "OD2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ASP 369": "OD1" <-> "OD2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 475": "OD1" <-> "OD2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C ASP 625": "OD1" <-> "OD2" Residue "C PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 667": "OE1" <-> "OE2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C ASP 681": "OD1" <-> "OD2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41242 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 30378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3802, 30320 Classifications: {'peptide': 3802} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 158, 'TRANS': 3641} Chain breaks: 15 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 17, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 128 Conformer: "B" Number of residues, atoms: 3802, 30320 Classifications: {'peptide': 3802} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 158, 'TRANS': 3641} Chain breaks: 15 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 17, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 128 bond proxies already assigned to first conformer: 30875 Chain: "B" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 496, 4009 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 27, 'TRANS': 468} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 496, 4009 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 27, 'TRANS': 468} Chain breaks: 1 bond proxies already assigned to first conformer: 4079 Chain: "C" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5354 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain: "F" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 383 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 70 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 70 " occ=0.50 residue: pdb=" N AARG A 257 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 257 " occ=0.50 Time building chain proxies: 35.40, per 1000 atoms: 0.86 Number of scatterers: 41242 At special positions: 0 Unit cell: (179.928, 167.433, 202.419, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 241 16.00 P 76 15.00 O 7745 8.00 N 7007 7.00 C 26173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.33 Conformation dependent library (CDL) restraints added in 12.8 seconds 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 231 helices and 12 sheets defined 53.9% alpha, 3.7% beta 34 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 28.58 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 4.095A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 43 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.750A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 79 through 95 removed outlier: 3.697A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.618A pdb=" N ALA A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Proline residue: A 102 - end of helix removed outlier: 5.314A pdb=" N VAL A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 112 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 117 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 149 through 161 removed outlier: 4.029A pdb=" N GLU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.641A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 217 through 230 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.871A pdb=" N ASP A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.546A pdb=" N CYS A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 407 through 423 Proline residue: A 411 - end of helix removed outlier: 3.810A pdb=" N LEU A 421 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.571A pdb=" N PHE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.792A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.979A pdb=" N ASN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 528 through 536 removed outlier: 3.547A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 542 No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 619 through 632 removed outlier: 4.484A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 659 removed outlier: 3.815A pdb=" N VAL A 646 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 648 " --> pdb=" O TRP A 645 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 649 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 658 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A 659 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 680 removed outlier: 3.642A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 720 removed outlier: 3.706A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 745 through 760 Proline residue: A 750 - end of helix removed outlier: 4.363A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 removed outlier: 3.594A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 removed outlier: 3.564A pdb=" N TYR A 789 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS A 790 " --> pdb=" O PRO A 787 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 791 " --> pdb=" O TYR A 788 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 792 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 793 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Proline residue: A 794 - end of helix No H-bonds generated for 'chain 'A' and resid 786 through 796' Processing helix chain 'A' and resid 819 through 822 No H-bonds generated for 'chain 'A' and resid 819 through 822' Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 867 through 869 No H-bonds generated for 'chain 'A' and resid 867 through 869' Processing helix chain 'A' and resid 876 through 882 removed outlier: 4.267A pdb=" N SER A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 919 Proline residue: A 912 - end of helix removed outlier: 3.617A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 945 Processing helix chain 'A' and resid 959 through 974 removed outlier: 4.012A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.848A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 995 Proline residue: A 986 - end of helix removed outlier: 3.739A pdb=" N MET A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1016 Processing helix chain 'A' and resid 1023 through 1040 removed outlier: 3.758A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1072 through 1090 removed outlier: 6.319A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1115 removed outlier: 3.631A pdb=" N GLU A1097 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1140 removed outlier: 3.785A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'A' and resid 1165 through 1174 Processing helix chain 'A' and resid 1181 through 1194 Processing helix chain 'A' and resid 1204 through 1213 Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.626A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1272 Processing helix chain 'A' and resid 1278 through 1282 removed outlier: 3.627A pdb=" N VAL A1281 " --> pdb=" O ALA A1278 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A1282 " --> pdb=" O LEU A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1278 through 1282' Processing helix chain 'A' and resid 1290 through 1300 Processing helix chain 'A' and resid 1325 through 1351 removed outlier: 4.077A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1379 through 1382 No H-bonds generated for 'chain 'A' and resid 1379 through 1382' Processing helix chain 'A' and resid 1390 through 1405 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1410 through 1422 removed outlier: 4.230A pdb=" N ASP A1413 " --> pdb=" O PRO A1410 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A1414 " --> pdb=" O TYR A1411 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1419 " --> pdb=" O GLU A1416 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A1420 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A1421 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1446 through 1461 removed outlier: 3.649A pdb=" N ALA A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1467 No H-bonds generated for 'chain 'A' and resid 1464 through 1467' Processing helix chain 'A' and resid 1480 through 1491 removed outlier: 4.160A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1521 Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1555 through 1562 Processing helix chain 'A' and resid 1566 through 1573 Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 4.146A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1606 removed outlier: 3.529A pdb=" N SER A1594 " --> pdb=" O THR A1590 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A1606 " --> pdb=" O ASP A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1624 removed outlier: 4.027A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1629 Processing helix chain 'A' and resid 1639 through 1655 removed outlier: 3.530A pdb=" N LEU A1646 " --> pdb=" O LYS A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1679 removed outlier: 3.529A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1692 removed outlier: 3.780A pdb=" N GLN A1691 " --> pdb=" O HIS A1687 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A1692 " --> pdb=" O LEU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1698 No H-bonds generated for 'chain 'A' and resid 1696 through 1698' Processing helix chain 'A' and resid 1706 through 1721 Processing helix chain 'A' and resid 1734 through 1752 removed outlier: 3.719A pdb=" N ASN A1738 " --> pdb=" O PRO A1734 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A1745 " --> pdb=" O ASP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1768 removed outlier: 3.942A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1786 Processing helix chain 'A' and resid 1793 through 1806 removed outlier: 3.700A pdb=" N LEU A1797 " --> pdb=" O THR A1793 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A1805 " --> pdb=" O VAL A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1821 removed outlier: 4.078A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1833 through 1851 removed outlier: 3.502A pdb=" N LEU A1836 " --> pdb=" O LEU A1833 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A1837 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU A1838 " --> pdb=" O ALA A1835 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A1839 " --> pdb=" O LEU A1836 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A1844 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL A1845 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A1846 " --> pdb=" O ILE A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1882 Processing helix chain 'A' and resid 1887 through 1890 No H-bonds generated for 'chain 'A' and resid 1887 through 1890' Processing helix chain 'A' and resid 1894 through 1899 removed outlier: 3.658A pdb=" N VAL A1899 " --> pdb=" O LYS A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1923 removed outlier: 3.591A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1955 removed outlier: 4.000A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1966 No H-bonds generated for 'chain 'A' and resid 1963 through 1966' Processing helix chain 'A' and resid 1978 through 1981 No H-bonds generated for 'chain 'A' and resid 1978 through 1981' Processing helix chain 'A' and resid 2094 through 2105 Processing helix chain 'A' and resid 2124 through 2133 removed outlier: 4.474A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2166 through 2172 Processing helix chain 'A' and resid 2184 through 2195 Processing helix chain 'A' and resid 2206 through 2221 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2253 through 2260 Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.789A pdb=" N VAL A2272 " --> pdb=" O ASP A2269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A2273 " --> pdb=" O ASN A2270 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A2281 " --> pdb=" O GLY A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2308 removed outlier: 4.243A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 4.480A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2336 through 2355 removed outlier: 4.275A pdb=" N SER A2340 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A2343 " --> pdb=" O SER A2340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A2346 " --> pdb=" O GLU A2343 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A2354 " --> pdb=" O GLN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2368 removed outlier: 3.832A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2374 No H-bonds generated for 'chain 'A' and resid 2372 through 2374' Processing helix chain 'A' and resid 2379 through 2386 removed outlier: 3.648A pdb=" N LEU A2385 " --> pdb=" O ALA A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2392 through 2403 removed outlier: 3.605A pdb=" N CYS A2403 " --> pdb=" O GLU A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2417 Processing helix chain 'A' and resid 2420 through 2424 Processing helix chain 'A' and resid 2429 through 2445 Proline residue: A2444 - end of helix Processing helix chain 'A' and resid 2448 through 2463 removed outlier: 3.905A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 4.167A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL A2462 " --> pdb=" O VAL A2458 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER A2463 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2467 through 2483 Processing helix chain 'A' and resid 2493 through 2511 removed outlier: 4.044A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE A2511 " --> pdb=" O ILE A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2517 through 2525 Processing helix chain 'A' and resid 2535 through 2544 removed outlier: 3.664A pdb=" N LEU A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2563 Processing helix chain 'A' and resid 2565 through 2568 removed outlier: 3.513A pdb=" N MET A2568 " --> pdb=" O MET A2565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2565 through 2568' Processing helix chain 'A' and resid 2736 through 2763 removed outlier: 3.710A pdb=" N LYS A2755 " --> pdb=" O GLN A2751 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A2756 " --> pdb=" O LYS A2752 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A2759 " --> pdb=" O LYS A2755 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS A2762 " --> pdb=" O LYS A2758 " (cutoff:3.500A) Processing helix chain 'A' and resid 2788 through 2798 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2802 through 2818 Processing helix chain 'A' and resid 2829 through 2846 removed outlier: 3.868A pdb=" N LYS A2835 " --> pdb=" O ASN A2831 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2860 Processing helix chain 'A' and resid 2866 through 2868 No H-bonds generated for 'chain 'A' and resid 2866 through 2868' Processing helix chain 'A' and resid 2873 through 2882 Processing helix chain 'A' and resid 2886 through 2897 Processing helix chain 'A' and resid 2920 through 2933 removed outlier: 3.722A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2941 removed outlier: 4.437A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2961 Processing helix chain 'A' and resid 2965 through 2976 removed outlier: 3.702A pdb=" N GLN A2971 " --> pdb=" O GLU A2967 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2988 through 3004 Processing helix chain 'A' and resid 3008 through 3016 Processing helix chain 'A' and resid 3027 through 3031 removed outlier: 3.908A pdb=" N TRP A3031 " --> pdb=" O ASN A3028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3035 through 3039 Processing helix chain 'A' and resid 3041 through 3053 Processing helix chain 'A' and resid 3061 through 3070 removed outlier: 4.046A pdb=" N HIS A3070 " --> pdb=" O ASP A3066 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3081 Processing helix chain 'A' and resid 3084 through 3092 Processing helix chain 'A' and resid 3096 through 3114 Processing helix chain 'A' and resid 3124 through 3129 Processing helix chain 'A' and resid 3132 through 3146 Processing helix chain 'A' and resid 3155 through 3166 removed outlier: 4.047A pdb=" N ASN A3166 " --> pdb=" O ASN A3162 " (cutoff:3.500A) Processing helix chain 'A' and resid 3176 through 3196 Processing helix chain 'A' and resid 3227 through 3248 Processing helix chain 'A' and resid 3252 through 3268 removed outlier: 3.747A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A3262 " --> pdb=" O LEU A3258 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A3263 " --> pdb=" O LEU A3259 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS A3264 " --> pdb=" O LYS A3260 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU A3265 " --> pdb=" O GLU A3261 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A3268 " --> pdb=" O LYS A3264 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3287 Processing helix chain 'A' and resid 3296 through 3303 removed outlier: 3.786A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3343 removed outlier: 3.676A pdb=" N SER A3342 " --> pdb=" O ALA A3338 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A3343 " --> pdb=" O ASN A3339 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3363 Processing helix chain 'A' and resid 3373 through 3392 Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 4.129A pdb=" N GLU A3427 " --> pdb=" O GLN A3423 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU A3428 " --> pdb=" O LEU A3424 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU A3429 " --> pdb=" O ARG A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3434 through 3439 Processing helix chain 'A' and resid 3442 through 3456 removed outlier: 4.205A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3462 No H-bonds generated for 'chain 'A' and resid 3459 through 3462' Processing helix chain 'A' and resid 3465 through 3471 Processing helix chain 'A' and resid 3481 through 3487 Processing helix chain 'A' and resid 3499 through 3507 removed outlier: 3.800A pdb=" N VAL A3503 " --> pdb=" O ILE A3499 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP A3507 " --> pdb=" O VAL A3503 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3524 Processing helix chain 'A' and resid 3530 through 3538 removed outlier: 4.549A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3561 Processing helix chain 'A' and resid 3567 through 3575 Processing helix chain 'A' and resid 3581 through 3596 Processing helix chain 'A' and resid 3607 through 3617 removed outlier: 4.304A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3629 through 3636 removed outlier: 3.844A pdb=" N THR A3635 " --> pdb=" O LYS A3631 " (cutoff:3.500A) Processing helix chain 'A' and resid 3656 through 3672 removed outlier: 4.163A pdb=" N LYS A3669 " --> pdb=" O MET A3665 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3683 No H-bonds generated for 'chain 'A' and resid 3680 through 3683' Processing helix chain 'A' and resid 3759 through 3774 Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.673A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3847 removed outlier: 4.342A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3859 removed outlier: 3.517A pdb=" N LEU A3857 " --> pdb=" O ALA A3854 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A3859 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3875 removed outlier: 3.752A pdb=" N SER A3870 " --> pdb=" O GLU A3866 " (cutoff:3.500A) Processing helix chain 'A' and resid 3883 through 3890 Processing helix chain 'A' and resid 3894 through 3917 removed outlier: 3.658A pdb=" N ILE A3913 " --> pdb=" O ALA A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3925 through 3927 No H-bonds generated for 'chain 'A' and resid 3925 through 3927' Processing helix chain 'A' and resid 3965 through 3968 No H-bonds generated for 'chain 'A' and resid 3965 through 3968' Processing helix chain 'A' and resid 3979 through 3991 Processing helix chain 'A' and resid 3996 through 4007 removed outlier: 4.879A pdb=" N ASP A4003 " --> pdb=" O THR A3999 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL A4004 " --> pdb=" O ASN A4000 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE A4005 " --> pdb=" O THR A4001 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A4006 " --> pdb=" O MET A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4011 through 4023 removed outlier: 4.557A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4027 through 4029 No H-bonds generated for 'chain 'A' and resid 4027 through 4029' Processing helix chain 'A' and resid 4039 through 4051 Processing helix chain 'A' and resid 4056 through 4067 Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4100 through 4111 removed outlier: 3.824A pdb=" N VAL A4104 " --> pdb=" O GLU A4100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A4109 " --> pdb=" O LYS A4105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A4110 " --> pdb=" O CYS A4106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A4111 " --> pdb=" O LEU A4107 " (cutoff:3.500A) Processing helix chain 'A' and resid 4114 through 4117 No H-bonds generated for 'chain 'A' and resid 4114 through 4117' Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'B' and resid 59 through 77 removed outlier: 4.194A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.697A pdb=" N LEU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.820A pdb=" N GLN B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.595A pdb=" N ALA B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 494 Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.785A pdb=" N ARG C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 108 through 114 removed outlier: 3.600A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.724A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 371 through 386 Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 485 through 499 removed outlier: 4.358A pdb=" N GLN C 492 " --> pdb=" O GLN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 520 through 523 No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 525 through 536 removed outlier: 4.027A pdb=" N ILE C 528 " --> pdb=" O LYS C 525 " (cutoff:3.500A) Proline residue: C 529 - end of helix removed outlier: 4.092A pdb=" N LYS C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 553 No H-bonds generated for 'chain 'C' and resid 550 through 553' Processing helix chain 'C' and resid 578 through 580 No H-bonds generated for 'chain 'C' and resid 578 through 580' Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 611 through 625 Processing helix chain 'C' and resid 629 through 649 removed outlier: 4.251A pdb=" N MET C 633 " --> pdb=" O THR C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 668 Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.898A pdb=" N ASP C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 583 through 585 Processing sheet with id= B, first strand: chain 'A' and resid 893 through 896 Processing sheet with id= C, first strand: chain 'A' and resid 3736 through 3741 removed outlier: 3.632A pdb=" N LEU A3800 " --> pdb=" O THR A3797 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id= E, first strand: chain 'B' and resid 102 through 104 removed outlier: 3.644A pdb=" N TYR B 88 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER B 37 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS B 164 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 39 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 166 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 41 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 168 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP B 43 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR B 170 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 260 through 262 Processing sheet with id= G, first strand: chain 'B' and resid 271 through 275 removed outlier: 3.716A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 431 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 322 Processing sheet with id= I, first strand: chain 'B' and resid 350 through 352 Processing sheet with id= J, first strand: chain 'C' and resid 224 through 226 removed outlier: 9.267A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 9 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU C 133 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL C 11 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE C 135 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS C 13 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 78 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 251 removed outlier: 6.437A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYS C 418 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 411 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 344 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 394 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 342 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA C 396 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N PHE C 340 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 313 through 315 1656 hydrogen bonds defined for protein. 4711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 30.35 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7270 1.32 - 1.45: 10842 1.45 - 1.58: 23590 1.58 - 1.70: 143 1.70 - 1.83: 382 Bond restraints: 42227 Sorted by residual: bond pdb=" C4 ATP A4201 " pdb=" C5 ATP A4201 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" C5 ATP A4201 " pdb=" C6 ATP A4201 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C8 ATP A4201 " pdb=" N7 ATP A4201 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C HIS A1721 " pdb=" N PHE A1722 " ideal model delta sigma weight residual 1.329 1.248 0.081 1.86e-02 2.89e+03 1.87e+01 bond pdb=" C5 ATP A4201 " pdb=" N7 ATP A4201 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.72e+01 ... (remaining 42222 not shown) Histogram of bond angle deviations from ideal: 95.87 - 104.87: 1037 104.87 - 113.87: 24369 113.87 - 122.88: 28929 122.88 - 131.88: 2927 131.88 - 140.88: 98 Bond angle restraints: 57360 Sorted by residual: angle pdb=" PB ATP A4201 " pdb=" O3B ATP A4201 " pdb=" PG ATP A4201 " ideal model delta sigma weight residual 139.87 120.42 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP A4201 " pdb=" O3A ATP A4201 " pdb=" PB ATP A4201 " ideal model delta sigma weight residual 136.83 120.50 16.33 1.00e+00 1.00e+00 2.67e+02 angle pdb=" C5 ATP A4201 " pdb=" C4 ATP A4201 " pdb=" N3 ATP A4201 " ideal model delta sigma weight residual 126.80 118.73 8.07 1.00e+00 1.00e+00 6.51e+01 angle pdb=" N3 ATP A4201 " pdb=" C4 ATP A4201 " pdb=" N9 ATP A4201 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 angle pdb=" C VAL A 8 " pdb=" N ARG A 9 " pdb=" CA ARG A 9 " ideal model delta sigma weight residual 121.54 133.13 -11.59 1.91e+00 2.74e-01 3.68e+01 ... (remaining 57355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 24806 35.98 - 71.97: 791 71.97 - 107.95: 75 107.95 - 143.93: 3 143.93 - 179.91: 3 Dihedral angle restraints: 25678 sinusoidal: 11034 harmonic: 14644 Sorted by residual: dihedral pdb=" CD BARG B 363 " pdb=" NE BARG B 363 " pdb=" CZ BARG B 363 " pdb=" NH1BARG B 363 " ideal model delta sinusoidal sigma weight residual 0.00 179.91 -179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA PHE A3694 " pdb=" C PHE A3694 " pdb=" N LEU A3695 " pdb=" CA LEU A3695 " ideal model delta harmonic sigma weight residual 180.00 133.87 46.13 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA ASP A3563 " pdb=" C ASP A3563 " pdb=" N GLN A3564 " pdb=" CA GLN A3564 " ideal model delta harmonic sigma weight residual 180.00 143.80 36.20 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 25675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.980: 6482 0.980 - 1.960: 0 1.960 - 2.941: 0 2.941 - 3.921: 0 3.921 - 4.901: 3 Chirality restraints: 6485 Sorted by residual: chirality pdb=" C2 IHP B 701 " pdb=" C1 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" O12 IHP B 701 " both_signs ideal model delta sigma weight residual False -2.52 2.38 -4.90 2.00e-01 2.50e+01 6.01e+02 chirality pdb=" C4 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" C5 IHP B 701 " pdb=" O14 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.48 -2.35 4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 IHP B 701 " pdb=" C2 IHP B 701 " pdb=" C6 IHP B 701 " pdb=" O11 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.77 2.00e-01 2.50e+01 5.69e+02 ... (remaining 6482 not shown) Planarity restraints: 7047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 9 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ARG A 9 " 0.078 2.00e-02 2.50e+03 pdb=" O ARG A 9 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS A 10 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A3893 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A3894 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A3894 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A3894 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 356 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ASN A 356 " -0.058 2.00e-02 2.50e+03 pdb=" O ASN A 356 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 357 " 0.020 2.00e-02 2.50e+03 ... (remaining 7044 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4915 2.74 - 3.28: 38886 3.28 - 3.82: 68872 3.82 - 4.36: 83366 4.36 - 4.90: 140350 Nonbonded interactions: 336389 Sorted by model distance: nonbonded pdb=" OH TYR A2546 " pdb=" OE2 GLU A2551 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A 366 " pdb=" OE2 GLU A 387 " model vdw 2.246 2.440 nonbonded pdb=" O SER A1753 " pdb=" OG SER A1753 " model vdw 2.256 2.440 nonbonded pdb=" O TYR A1560 " pdb=" OG SER A1564 " model vdw 2.264 2.440 nonbonded pdb=" O SER A3731 " pdb=" OG SER A3731 " model vdw 2.280 2.440 ... (remaining 336384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.910 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: 25.630 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 148.840 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.010 0.120 42227 Z= 0.655 Angle : 1.149 19.446 57360 Z= 0.619 Chirality : 0.122 4.901 6485 Planarity : 0.008 0.095 7047 Dihedral : 17.553 179.913 16136 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.45 % Favored : 90.31 % Rotamer: Outliers : 0.29 % Allowed : 8.47 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.15 % 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: -4.26 (0.09), residues: 4933 helix: -2.50 (0.07), residues: 2859 sheet: -1.46 (0.34), residues: 217 loop : -3.37 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 813 HIS 0.016 0.002 HIS A3915 PHE 0.050 0.003 PHE A1923 TYR 0.031 0.003 TYR A3082 ARG 0.013 0.001 ARG A2899 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 469 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.8572 (ttm) cc_final: 0.8336 (ttm) REVERT: A 1353 PRO cc_start: 0.6741 (Cg_endo) cc_final: 0.6512 (Cg_exo) REVERT: A 1378 GLU cc_start: 0.7172 (tp30) cc_final: 0.6902 (tp30) REVERT: A 1719 VAL cc_start: 0.8220 (m) cc_final: 0.7946 (t) REVERT: A 1739 TYR cc_start: 0.7921 (t80) cc_final: 0.7568 (t80) REVERT: A 1814 PHE cc_start: 0.7106 (t80) cc_final: 0.6896 (t80) REVERT: A 2294 ILE cc_start: 0.7266 (mm) cc_final: 0.6648 (mm) REVERT: A 2742 MET cc_start: 0.6837 (mmt) cc_final: 0.6600 (mmt) REVERT: A 2772 TYR cc_start: 0.7332 (m-80) cc_final: 0.7037 (m-80) REVERT: A 3104 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7119 (tp40) REVERT: B 131 PHE cc_start: 0.7922 (t80) cc_final: 0.7566 (t80) REVERT: B 134 MET cc_start: 0.6033 (ppp) cc_final: 0.5094 (ppp) REVERT: B 135 MET cc_start: 0.5262 (tpp) cc_final: 0.4902 (mmm) REVERT: B 530 TYR cc_start: 0.5131 (t80) cc_final: 0.4479 (t80) REVERT: C 14 MET cc_start: 0.4957 (ttm) cc_final: 0.4730 (tmm) REVERT: C 183 PHE cc_start: 0.4564 (t80) cc_final: 0.4136 (t80) outliers start: 9 outliers final: 5 residues processed: 477 average time/residue: 0.5920 time to fit residues: 464.2903 Evaluate side-chains 370 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 365 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 6.9990 chunk 378 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 255 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 391 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 238 optimal weight: 0.2980 chunk 291 optimal weight: 1.9990 chunk 454 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1175 HIS A1374 GLN A1654 GLN A1859 ASN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN A2183 HIS A2390 HIS A2475 ASN A2574 ASN A2736 GLN A2777 HIS A3384 HIS A3430 ASN A3457 ASN A3697 ASN B 68 GLN B 152 ASN C 43 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN C 411 HIS C 547 GLN C 627 ASN C 680 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42227 Z= 0.177 Angle : 0.615 12.583 57360 Z= 0.315 Chirality : 0.041 0.558 6485 Planarity : 0.005 0.077 7047 Dihedral : 13.545 179.641 6183 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 1.00 % Allowed : 11.09 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 4933 helix: -0.74 (0.09), residues: 2865 sheet: -0.89 (0.36), residues: 216 loop : -3.06 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1256 HIS 0.007 0.001 HIS A3549 PHE 0.032 0.001 PHE A1553 TYR 0.022 0.001 TYR A2288 ARG 0.005 0.000 ARG A2596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 4.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 GLU cc_start: 0.6480 (pt0) cc_final: 0.5839 (tp30) REVERT: A 1197 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8317 (pp) REVERT: A 1353 PRO cc_start: 0.6722 (Cg_endo) cc_final: 0.6503 (Cg_exo) REVERT: A 1467 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (mp) REVERT: A 1739 TYR cc_start: 0.7907 (t80) cc_final: 0.7528 (t80) REVERT: A 2083 LEU cc_start: 0.7616 (pt) cc_final: 0.7289 (pt) REVERT: A 2294 ILE cc_start: 0.7013 (mm) cc_final: 0.6622 (mm) REVERT: A 2596 ARG cc_start: 0.5449 (ttt90) cc_final: 0.5187 (tpt-90) REVERT: A 2742 MET cc_start: 0.6968 (mmt) cc_final: 0.6764 (mmt) REVERT: A 2860 ASP cc_start: 0.8379 (t70) cc_final: 0.8001 (t0) REVERT: A 3104 GLN cc_start: 0.7230 (mm-40) cc_final: 0.7015 (tp40) REVERT: A 3429 GLU cc_start: 0.6327 (mp0) cc_final: 0.6077 (mp0) REVERT: A 3654 MET cc_start: 0.5374 (ptm) cc_final: 0.5089 (ttm) REVERT: A 4019 LYS cc_start: 0.6706 (mtmt) cc_final: 0.6448 (mtmt) REVERT: B 131 PHE cc_start: 0.7870 (t80) cc_final: 0.7517 (t80) REVERT: B 134 MET cc_start: 0.5935 (ppp) cc_final: 0.5089 (ppp) REVERT: C 183 PHE cc_start: 0.4579 (t80) cc_final: 0.4205 (t80) REVERT: C 611 GLU cc_start: 0.2753 (OUTLIER) cc_final: 0.2139 (pt0) outliers start: 40 outliers final: 16 residues processed: 450 average time/residue: 0.5472 time to fit residues: 409.2315 Evaluate side-chains 376 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 357 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 chunk 491 optimal weight: 10.0000 chunk 405 optimal weight: 5.9990 chunk 451 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 HIS A1932 GLN ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2736 GLN A4015 ASN C 269 GLN C 411 HIS C 627 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 42227 Z= 0.364 Angle : 0.689 10.225 57360 Z= 0.352 Chirality : 0.045 0.356 6485 Planarity : 0.005 0.076 7047 Dihedral : 13.750 179.523 6182 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.92 % Favored : 91.00 % Rotamer: Outliers : 1.77 % Allowed : 12.66 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -1.91 (0.12), residues: 4933 helix: -0.34 (0.10), residues: 2866 sheet: -0.84 (0.35), residues: 228 loop : -2.81 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 813 HIS 0.010 0.001 HIS A3915 PHE 0.042 0.002 PHE A1553 TYR 0.029 0.002 TYR A3082 ARG 0.005 0.001 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 363 time to evaluate : 4.713 Fit side-chains revert: symmetry clash REVERT: A 396 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8395 (p90) REVERT: A 827 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8087 (p0) REVERT: A 1197 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8318 (pp) REVERT: A 1353 PRO cc_start: 0.6725 (Cg_endo) cc_final: 0.6473 (Cg_exo) REVERT: A 1369 MET cc_start: 0.8413 (mmt) cc_final: 0.8132 (mmt) REVERT: A 1467 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8860 (mp) REVERT: A 1739 TYR cc_start: 0.7914 (t80) cc_final: 0.7576 (t80) REVERT: A 2083 LEU cc_start: 0.7717 (pt) cc_final: 0.7412 (pt) REVERT: A 2127 LYS cc_start: 0.7444 (mmmt) cc_final: 0.7095 (mmtp) REVERT: A 2294 ILE cc_start: 0.7106 (mm) cc_final: 0.6670 (mm) REVERT: A 2742 MET cc_start: 0.6973 (mmt) cc_final: 0.6752 (mmt) REVERT: A 2772 TYR cc_start: 0.7603 (m-80) cc_final: 0.6968 (m-80) REVERT: A 3429 GLU cc_start: 0.6426 (mp0) cc_final: 0.6212 (mp0) REVERT: A 3472 ILE cc_start: 0.7242 (mm) cc_final: 0.7025 (mt) REVERT: A 3654 MET cc_start: 0.5367 (ptm) cc_final: 0.5165 (ttm) REVERT: A 3858 MET cc_start: 0.7329 (ppp) cc_final: 0.7127 (ttp) REVERT: B 134 MET cc_start: 0.5968 (ppp) cc_final: 0.5289 (ppp) REVERT: C 142 PHE cc_start: 0.3273 (m-80) cc_final: 0.3025 (m-80) REVERT: C 183 PHE cc_start: 0.4560 (t80) cc_final: 0.4180 (t80) REVERT: C 611 GLU cc_start: 0.2842 (OUTLIER) cc_final: 0.2089 (pt0) outliers start: 74 outliers final: 49 residues processed: 423 average time/residue: 0.5378 time to fit residues: 384.4511 Evaluate side-chains 406 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 352 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1681 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2492 ASP Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3379 GLN Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4006 VAL Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 659 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 0.7980 chunk 341 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 305 optimal weight: 0.0470 chunk 456 optimal weight: 6.9990 chunk 483 optimal weight: 20.0000 chunk 238 optimal weight: 0.8980 chunk 432 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN A1476 HIS A1716 GLN A1974 ASN A1989 ASN A2736 GLN A3783 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 42227 Z= 0.174 Angle : 0.566 9.568 57360 Z= 0.290 Chirality : 0.040 0.223 6485 Planarity : 0.004 0.069 7047 Dihedral : 13.308 179.592 6182 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.93 % Favored : 93.03 % Rotamer: Outliers : 1.31 % Allowed : 13.83 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -1.33 (0.12), residues: 4933 helix: 0.22 (0.10), residues: 2852 sheet: -0.52 (0.35), residues: 233 loop : -2.72 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1256 HIS 0.007 0.001 HIS A3549 PHE 0.040 0.001 PHE A1553 TYR 0.021 0.001 TYR B 530 ARG 0.006 0.000 ARG A2596 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 394 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 GLU cc_start: 0.6533 (pt0) cc_final: 0.5861 (tp30) REVERT: A 958 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7411 (mtm) REVERT: A 1197 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8305 (pp) REVERT: A 1353 PRO cc_start: 0.6622 (Cg_endo) cc_final: 0.6376 (Cg_exo) REVERT: A 1467 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8910 (mp) REVERT: A 1739 TYR cc_start: 0.7902 (t80) cc_final: 0.7547 (t80) REVERT: A 1920 TYR cc_start: 0.6831 (t80) cc_final: 0.6178 (t80) REVERT: A 2083 LEU cc_start: 0.7597 (pt) cc_final: 0.7279 (pt) REVERT: A 2127 LYS cc_start: 0.7353 (mmmt) cc_final: 0.7112 (mmtp) REVERT: A 2294 ILE cc_start: 0.6993 (mm) cc_final: 0.6564 (mm) REVERT: A 2742 MET cc_start: 0.7041 (mmt) cc_final: 0.6804 (mmt) REVERT: A 2772 TYR cc_start: 0.7483 (m-80) cc_final: 0.6906 (m-80) REVERT: A 2860 ASP cc_start: 0.8376 (t70) cc_final: 0.7965 (t0) REVERT: B 134 MET cc_start: 0.5940 (ppp) cc_final: 0.5128 (ppp) REVERT: B 530 TYR cc_start: 0.4866 (t80) cc_final: 0.4407 (t80) REVERT: C 183 PHE cc_start: 0.4592 (t80) cc_final: 0.4260 (t80) REVERT: C 611 GLU cc_start: 0.2782 (OUTLIER) cc_final: 0.2020 (pt0) outliers start: 54 outliers final: 36 residues processed: 434 average time/residue: 0.5300 time to fit residues: 386.2304 Evaluate side-chains 405 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 365 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 0.9990 chunk 274 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 199 optimal weight: 0.0070 chunk 412 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 433 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 HIS A1716 GLN ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2103 HIS B 152 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 42227 Z= 0.197 Angle : 0.570 9.139 57360 Z= 0.291 Chirality : 0.040 0.273 6485 Planarity : 0.004 0.067 7047 Dihedral : 13.258 179.909 6182 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.58 % Favored : 92.38 % Rotamer: Outliers : 1.72 % Allowed : 14.49 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -1.09 (0.12), residues: 4933 helix: 0.42 (0.10), residues: 2845 sheet: -0.42 (0.35), residues: 233 loop : -2.63 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1256 HIS 0.006 0.001 HIS A3549 PHE 0.033 0.001 PHE A3554 TYR 0.018 0.001 TYR B 530 ARG 0.004 0.000 ARG A2596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 377 time to evaluate : 4.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 GLU cc_start: 0.6520 (pt0) cc_final: 0.5826 (tp30) REVERT: A 1197 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8310 (pp) REVERT: A 1353 PRO cc_start: 0.6557 (Cg_endo) cc_final: 0.6263 (Cg_exo) REVERT: A 1467 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8920 (mp) REVERT: A 1739 TYR cc_start: 0.7895 (t80) cc_final: 0.7517 (t80) REVERT: A 1920 TYR cc_start: 0.6846 (t80) cc_final: 0.6159 (t80) REVERT: A 2083 LEU cc_start: 0.7609 (pt) cc_final: 0.7273 (pt) REVERT: A 2127 LYS cc_start: 0.7393 (mmmt) cc_final: 0.7166 (mmtp) REVERT: A 2294 ILE cc_start: 0.7020 (mm) cc_final: 0.6588 (mm) REVERT: A 2742 MET cc_start: 0.7048 (mmt) cc_final: 0.6812 (mmt) REVERT: A 2772 TYR cc_start: 0.7529 (m-80) cc_final: 0.6992 (m-80) REVERT: A 2860 ASP cc_start: 0.8370 (t70) cc_final: 0.7970 (t0) REVERT: B 134 MET cc_start: 0.5945 (ppp) cc_final: 0.5151 (ppp) REVERT: B 530 TYR cc_start: 0.4872 (t80) cc_final: 0.4427 (t80) REVERT: C 142 PHE cc_start: 0.3303 (m-80) cc_final: 0.3069 (m-80) REVERT: C 183 PHE cc_start: 0.4636 (t80) cc_final: 0.4290 (t80) REVERT: C 611 GLU cc_start: 0.2805 (OUTLIER) cc_final: 0.2009 (pt0) outliers start: 72 outliers final: 52 residues processed: 431 average time/residue: 0.5373 time to fit residues: 390.1116 Evaluate side-chains 418 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 363 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3729 MET Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 283 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 483 optimal weight: 20.0000 chunk 401 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 253 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1476 HIS A1716 GLN ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 42227 Z= 0.153 Angle : 0.543 11.337 57360 Z= 0.276 Chirality : 0.039 0.266 6485 Planarity : 0.004 0.063 7047 Dihedral : 13.038 179.701 6182 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 1.68 % Allowed : 15.06 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4933 helix: 0.65 (0.10), residues: 2841 sheet: -0.28 (0.35), residues: 234 loop : -2.59 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1256 HIS 0.005 0.001 HIS A3549 PHE 0.035 0.001 PHE A3554 TYR 0.018 0.001 TYR B 530 ARG 0.004 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 398 time to evaluate : 4.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: A 878 GLU cc_start: 0.6443 (pt0) cc_final: 0.5764 (tp30) REVERT: A 958 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7472 (mtm) REVERT: A 1197 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 1353 PRO cc_start: 0.6402 (Cg_endo) cc_final: 0.6097 (Cg_exo) REVERT: A 1640 GLU cc_start: 0.8146 (pm20) cc_final: 0.7928 (pm20) REVERT: A 1665 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.4662 (p-80) REVERT: A 1739 TYR cc_start: 0.7906 (t80) cc_final: 0.7568 (t80) REVERT: A 1920 TYR cc_start: 0.6831 (t80) cc_final: 0.6214 (t80) REVERT: A 2083 LEU cc_start: 0.7544 (pt) cc_final: 0.7206 (pt) REVERT: A 2294 ILE cc_start: 0.6996 (mm) cc_final: 0.6609 (mm) REVERT: A 2742 MET cc_start: 0.7033 (mmt) cc_final: 0.6809 (mmt) REVERT: A 2860 ASP cc_start: 0.8329 (t70) cc_final: 0.7976 (t0) REVERT: A 3383 GLN cc_start: 0.8068 (tt0) cc_final: 0.7713 (mp10) REVERT: A 3613 MET cc_start: 0.6179 (tmm) cc_final: 0.5682 (tmm) REVERT: A 3747 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7553 (mt-10) REVERT: B 134 MET cc_start: 0.5828 (ppp) cc_final: 0.4950 (ppp) REVERT: B 473 TYR cc_start: 0.7049 (t80) cc_final: 0.6734 (t80) REVERT: B 530 TYR cc_start: 0.4810 (t80) cc_final: 0.4507 (t80) REVERT: C 24 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4593 (tp) REVERT: C 40 MET cc_start: 0.6856 (ttp) cc_final: 0.6616 (ttt) REVERT: C 183 PHE cc_start: 0.4578 (t80) cc_final: 0.4283 (t80) REVERT: C 320 ILE cc_start: 0.8288 (mt) cc_final: 0.8072 (mt) REVERT: C 611 GLU cc_start: 0.2835 (OUTLIER) cc_final: 0.2101 (pt0) outliers start: 70 outliers final: 48 residues processed: 453 average time/residue: 0.5371 time to fit residues: 409.4454 Evaluate side-chains 421 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 367 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2283 ASN Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3165 THR Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3968 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 273 optimal weight: 0.0070 chunk 407 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 481 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1374 GLN A1476 HIS A1716 GLN A1770 GLN ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2736 GLN A3762 GLN B 152 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42227 Z= 0.272 Angle : 0.610 9.426 57360 Z= 0.309 Chirality : 0.042 0.272 6485 Planarity : 0.004 0.064 7047 Dihedral : 13.264 179.872 6182 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.99 % Rotamer: Outliers : 2.06 % Allowed : 15.21 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4933 helix: 0.52 (0.10), residues: 2857 sheet: -0.34 (0.34), residues: 237 loop : -2.52 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2125 HIS 0.006 0.001 HIS A3915 PHE 0.033 0.002 PHE A3554 TYR 0.022 0.002 TYR A3082 ARG 0.005 0.000 ARG A2538 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 368 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8232 (p90) REVERT: A 628 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 805 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.5016 (tt) REVERT: A 878 GLU cc_start: 0.6419 (pt0) cc_final: 0.5738 (tp30) REVERT: A 1197 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8313 (pp) REVERT: A 1353 PRO cc_start: 0.6456 (Cg_endo) cc_final: 0.6158 (Cg_exo) REVERT: A 1665 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.4721 (p-80) REVERT: A 1739 TYR cc_start: 0.7918 (t80) cc_final: 0.7535 (t80) REVERT: A 2083 LEU cc_start: 0.7620 (pt) cc_final: 0.7290 (pt) REVERT: A 2294 ILE cc_start: 0.7153 (mm) cc_final: 0.6740 (mm) REVERT: A 2742 MET cc_start: 0.7054 (mmt) cc_final: 0.6804 (mmt) REVERT: A 2772 TYR cc_start: 0.7569 (m-80) cc_final: 0.7082 (m-80) REVERT: A 2860 ASP cc_start: 0.8386 (t70) cc_final: 0.7984 (t0) REVERT: B 134 MET cc_start: 0.5888 (ppp) cc_final: 0.5006 (ppp) REVERT: B 530 TYR cc_start: 0.5024 (t80) cc_final: 0.4596 (t80) REVERT: C 40 MET cc_start: 0.6906 (ttp) cc_final: 0.6658 (ttt) REVERT: C 142 PHE cc_start: 0.3562 (m-80) cc_final: 0.3263 (m-80) REVERT: C 183 PHE cc_start: 0.4751 (t80) cc_final: 0.4444 (t80) REVERT: C 604 GLN cc_start: 0.1028 (OUTLIER) cc_final: 0.0819 (pp30) REVERT: C 611 GLU cc_start: 0.2852 (OUTLIER) cc_final: 0.2000 (pt0) outliers start: 87 outliers final: 67 residues processed: 435 average time/residue: 0.5256 time to fit residues: 387.5796 Evaluate side-chains 431 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 357 time to evaluate : 4.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2283 ASN Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3165 THR Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 659 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 238 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 chunk 378 optimal weight: 0.0030 overall best weight: 0.8050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1374 GLN A1716 GLN ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2348 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 42227 Z= 0.157 Angle : 0.547 9.668 57360 Z= 0.278 Chirality : 0.039 0.259 6485 Planarity : 0.004 0.063 7047 Dihedral : 12.991 179.869 6182 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 1.65 % Allowed : 15.85 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 4933 helix: 0.74 (0.10), residues: 2855 sheet: -0.26 (0.34), residues: 239 loop : -2.50 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2125 HIS 0.005 0.001 HIS A3549 PHE 0.034 0.001 PHE A3554 TYR 0.016 0.001 TYR B 530 ARG 0.004 0.000 ARG A1245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 385 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 878 GLU cc_start: 0.6380 (pt0) cc_final: 0.5719 (tp30) REVERT: A 958 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7498 (mtm) REVERT: A 1118 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: A 1197 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8359 (pp) REVERT: A 1353 PRO cc_start: 0.6480 (Cg_endo) cc_final: 0.6125 (Cg_exo) REVERT: A 1640 GLU cc_start: 0.8192 (pm20) cc_final: 0.7845 (pm20) REVERT: A 1665 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.4624 (p-80) REVERT: A 1739 TYR cc_start: 0.7916 (t80) cc_final: 0.7510 (t80) REVERT: A 1920 TYR cc_start: 0.6796 (t80) cc_final: 0.6296 (t80) REVERT: A 2083 LEU cc_start: 0.7547 (pt) cc_final: 0.7214 (pt) REVERT: A 2294 ILE cc_start: 0.7067 (mm) cc_final: 0.6587 (mm) REVERT: A 2742 MET cc_start: 0.7025 (mmt) cc_final: 0.6796 (mmt) REVERT: A 2860 ASP cc_start: 0.8336 (t70) cc_final: 0.7969 (t0) REVERT: A 3383 GLN cc_start: 0.8089 (tt0) cc_final: 0.7706 (mp10) REVERT: A 3613 MET cc_start: 0.6232 (tmm) cc_final: 0.5594 (tmm) REVERT: A 3747 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 131 PHE cc_start: 0.8031 (t80) cc_final: 0.7715 (t80) REVERT: B 134 MET cc_start: 0.5809 (ppp) cc_final: 0.4978 (ppp) REVERT: B 473 TYR cc_start: 0.7003 (t80) cc_final: 0.6727 (t80) REVERT: B 530 TYR cc_start: 0.4916 (t80) cc_final: 0.4593 (t80) REVERT: C 40 MET cc_start: 0.6873 (ttp) cc_final: 0.6658 (ttt) REVERT: C 183 PHE cc_start: 0.4710 (t80) cc_final: 0.4430 (t80) REVERT: C 320 ILE cc_start: 0.8319 (mt) cc_final: 0.8109 (mt) REVERT: C 611 GLU cc_start: 0.2859 (OUTLIER) cc_final: 0.2059 (pt0) outliers start: 69 outliers final: 52 residues processed: 440 average time/residue: 0.5325 time to fit residues: 393.9075 Evaluate side-chains 432 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 374 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2092 GLU Chi-restraints excluded: chain A residue 2283 ASN Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3165 THR Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 9.9990 chunk 461 optimal weight: 10.0000 chunk 421 optimal weight: 4.9990 chunk 449 optimal weight: 0.0980 chunk 270 optimal weight: 5.9990 chunk 195 optimal weight: 0.0270 chunk 352 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 405 optimal weight: 0.0050 chunk 424 optimal weight: 0.4980 chunk 447 optimal weight: 0.5980 overall best weight: 0.2452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 978 GLN A1476 HIS A1721 HIS ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2574 ASN ** A3716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3951 GLN C 104 GLN ** C 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 42227 Z= 0.145 Angle : 0.535 11.462 57360 Z= 0.271 Chirality : 0.038 0.252 6485 Planarity : 0.004 0.061 7047 Dihedral : 12.726 179.753 6182 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 1.29 % Allowed : 16.32 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4933 helix: 0.99 (0.10), residues: 2868 sheet: 0.02 (0.35), residues: 232 loop : -2.45 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A3493 HIS 0.008 0.001 HIS C 619 PHE 0.034 0.001 PHE A3382 TYR 0.018 0.001 TYR A1945 ARG 0.005 0.000 ARG A2333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 427 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 LYS cc_start: 0.6566 (tptt) cc_final: 0.6280 (tptt) REVERT: A 628 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 788 TYR cc_start: 0.7849 (m-80) cc_final: 0.7589 (m-80) REVERT: A 878 GLU cc_start: 0.6295 (pt0) cc_final: 0.5651 (tp30) REVERT: A 958 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7465 (mtm) REVERT: A 1118 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: A 1197 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 1353 PRO cc_start: 0.6456 (Cg_endo) cc_final: 0.6055 (Cg_exo) REVERT: A 1640 GLU cc_start: 0.8181 (pm20) cc_final: 0.7826 (pm20) REVERT: A 1739 TYR cc_start: 0.7852 (t80) cc_final: 0.7441 (t80) REVERT: A 2083 LEU cc_start: 0.7498 (pt) cc_final: 0.7150 (pt) REVERT: A 2294 ILE cc_start: 0.7096 (mm) cc_final: 0.6677 (mm) REVERT: A 2742 MET cc_start: 0.7052 (mmt) cc_final: 0.6834 (mmt) REVERT: A 2860 ASP cc_start: 0.8310 (t70) cc_final: 0.7983 (t0) REVERT: A 3383 GLN cc_start: 0.7919 (tt0) cc_final: 0.7658 (mp10) REVERT: A 3413 TYR cc_start: 0.8449 (m-10) cc_final: 0.8071 (m-10) REVERT: A 3613 MET cc_start: 0.6029 (tmm) cc_final: 0.5458 (tmm) REVERT: A 3747 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 4006 VAL cc_start: 0.7867 (p) cc_final: 0.7624 (p) REVERT: B 131 PHE cc_start: 0.7975 (t80) cc_final: 0.7670 (t80) REVERT: B 134 MET cc_start: 0.5915 (ppp) cc_final: 0.5079 (ppp) REVERT: B 530 TYR cc_start: 0.4958 (t80) cc_final: 0.4685 (t80) REVERT: C 40 MET cc_start: 0.6885 (ttp) cc_final: 0.6647 (ttt) REVERT: C 59 PHE cc_start: 0.4855 (p90) cc_final: 0.4517 (p90) REVERT: C 183 PHE cc_start: 0.4688 (t80) cc_final: 0.4417 (t80) REVERT: C 320 ILE cc_start: 0.8286 (mt) cc_final: 0.8084 (mt) REVERT: C 457 LEU cc_start: 0.8158 (tp) cc_final: 0.7770 (tt) REVERT: C 611 GLU cc_start: 0.2508 (OUTLIER) cc_final: 0.1635 (pt0) outliers start: 53 outliers final: 36 residues processed: 468 average time/residue: 0.5456 time to fit residues: 430.2358 Evaluate side-chains 428 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 387 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1553 PHE Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3165 THR Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 0.2980 chunk 474 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 498 optimal weight: 10.0000 chunk 458 optimal weight: 7.9990 chunk 396 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A1374 GLN A1476 HIS ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN B 426 GLN ** C 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 42227 Z= 0.197 Angle : 0.569 13.079 57360 Z= 0.287 Chirality : 0.040 0.248 6485 Planarity : 0.004 0.062 7047 Dihedral : 12.853 179.564 6182 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 1.31 % Allowed : 16.46 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4933 helix: 0.90 (0.10), residues: 2887 sheet: -0.06 (0.35), residues: 234 loop : -2.39 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2125 HIS 0.008 0.001 HIS C 496 PHE 0.031 0.001 PHE A3554 TYR 0.022 0.001 TYR B 473 ARG 0.006 0.000 ARG B 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 378 time to evaluate : 4.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 878 GLU cc_start: 0.6325 (pt0) cc_final: 0.5718 (tp30) REVERT: A 1118 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: A 1197 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8374 (pp) REVERT: A 1353 PRO cc_start: 0.6408 (Cg_endo) cc_final: 0.6022 (Cg_exo) REVERT: A 1640 GLU cc_start: 0.8206 (pm20) cc_final: 0.7807 (pm20) REVERT: A 1739 TYR cc_start: 0.7886 (t80) cc_final: 0.7512 (t80) REVERT: A 2083 LEU cc_start: 0.7503 (pt) cc_final: 0.7165 (pt) REVERT: A 2294 ILE cc_start: 0.7042 (mm) cc_final: 0.6605 (mm) REVERT: A 2742 MET cc_start: 0.7049 (mmt) cc_final: 0.6829 (mmt) REVERT: A 2860 ASP cc_start: 0.8369 (t70) cc_final: 0.8003 (t0) REVERT: A 3383 GLN cc_start: 0.7802 (tt0) cc_final: 0.7541 (mp10) REVERT: A 3413 TYR cc_start: 0.8459 (m-10) cc_final: 0.8076 (m-10) REVERT: A 3613 MET cc_start: 0.6148 (tmm) cc_final: 0.5502 (tmm) REVERT: A 4006 VAL cc_start: 0.7887 (p) cc_final: 0.7635 (p) REVERT: B 131 PHE cc_start: 0.7981 (t80) cc_final: 0.7637 (t80) REVERT: B 134 MET cc_start: 0.5909 (ppp) cc_final: 0.5091 (ppp) REVERT: B 530 TYR cc_start: 0.4965 (t80) cc_final: 0.4612 (t80) REVERT: C 40 MET cc_start: 0.6830 (ttp) cc_final: 0.6624 (ttt) REVERT: C 183 PHE cc_start: 0.4794 (t80) cc_final: 0.4488 (t80) REVERT: C 457 LEU cc_start: 0.8123 (tp) cc_final: 0.7921 (tt) REVERT: C 611 GLU cc_start: 0.2538 (OUTLIER) cc_final: 0.1759 (pt0) outliers start: 54 outliers final: 40 residues processed: 423 average time/residue: 0.5372 time to fit residues: 383.7775 Evaluate side-chains 417 residues out of total 4444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 373 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1553 PHE Chi-restraints excluded: chain A residue 1576 ASP Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3165 THR Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 3.9990 chunk 422 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.0270 chunk 397 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN ** C 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102920 restraints weight = 191265.288| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 5.24 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 42227 Z= 0.170 Angle : 0.551 9.911 57360 Z= 0.279 Chirality : 0.039 0.248 6485 Planarity : 0.004 0.062 7047 Dihedral : 12.817 179.919 6182 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 1.29 % Allowed : 16.55 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4933 helix: 0.93 (0.10), residues: 2879 sheet: -0.03 (0.35), residues: 234 loop : -2.34 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2125 HIS 0.009 0.001 HIS C 496 PHE 0.031 0.001 PHE A3554 TYR 0.024 0.001 TYR B 473 ARG 0.004 0.000 ARG A1608 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8958.17 seconds wall clock time: 163 minutes 12.00 seconds (9792.00 seconds total)