Starting phenix.real_space_refine on Tue May 14 01:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/05_2024/8x15_37984_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/05_2024/8x15_37984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/05_2024/8x15_37984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/05_2024/8x15_37984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/05_2024/8x15_37984_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/05_2024/8x15_37984_neut_updated.pdb" } resolution = 3.2 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= 0.004 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 291 5.49 5 S 252 5.16 5 C 34081 2.51 5 N 9849 2.21 5 O 11015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 83": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 52": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I ARG 163": "NH1" <-> "NH2" Residue "I ARG 167": "NH1" <-> "NH2" Residue "I ARG 171": "NH1" <-> "NH2" Residue "I ARG 177": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 184": "NH1" <-> "NH2" Residue "I ARG 185": "NH1" <-> "NH2" Residue "I ARG 192": "NH1" <-> "NH2" Residue "I ARG 193": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 225": "NH1" <-> "NH2" Residue "I ARG 615": "NH1" <-> "NH2" Residue "I ARG 619": "NH1" <-> "NH2" Residue "I TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 688": "NH1" <-> "NH2" Residue "I ARG 705": "NH1" <-> "NH2" Residue "I ARG 709": "NH1" <-> "NH2" Residue "I PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 736": "NH1" <-> "NH2" Residue "I ARG 737": "NH1" <-> "NH2" Residue "I ARG 741": "NH1" <-> "NH2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 758": "NH1" <-> "NH2" Residue "I ARG 769": "NH1" <-> "NH2" Residue "I ARG 770": "NH1" <-> "NH2" Residue "I ARG 858": "NH1" <-> "NH2" Residue "I ARG 860": "NH1" <-> "NH2" Residue "I ARG 864": "NH1" <-> "NH2" Residue "I ARG 866": "NH1" <-> "NH2" Residue "I ARG 898": "NH1" <-> "NH2" Residue "I ARG 910": "NH1" <-> "NH2" Residue "I PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 931": "NH1" <-> "NH2" Residue "I ARG 940": "NH1" <-> "NH2" Residue "I ARG 945": "NH1" <-> "NH2" Residue "I ARG 954": "NH1" <-> "NH2" Residue "I ARG 957": "NH1" <-> "NH2" Residue "I TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 966": "NH1" <-> "NH2" Residue "I ARG 968": "NH1" <-> "NH2" Residue "I ARG 971": "NH1" <-> "NH2" Residue "I ARG 972": "NH1" <-> "NH2" Residue "I GLU 976": "OE1" <-> "OE2" Residue "I ARG 986": "NH1" <-> "NH2" Residue "I ARG 1893": "NH1" <-> "NH2" Residue "I ARG 1895": "NH1" <-> "NH2" Residue "I ARG 1897": "NH1" <-> "NH2" Residue "I ARG 1900": "NH1" <-> "NH2" Residue "I ARG 1903": "NH1" <-> "NH2" Residue "I ARG 1939": "NH1" <-> "NH2" Residue "I ARG 1957": "NH1" <-> "NH2" Residue "I ARG 1965": "NH1" <-> "NH2" Residue "I ARG 1975": "NH1" <-> "NH2" Residue "I PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 2002": "NH1" <-> "NH2" Residue "I ARG 2017": "NH1" <-> "NH2" Residue "I ARG 2019": "NH1" <-> "NH2" Residue "I ARG 2023": "NH1" <-> "NH2" Residue "I ARG 2029": "NH1" <-> "NH2" Residue "I PHE 2032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 2036": "NH1" <-> "NH2" Residue "I ARG 2053": "NH1" <-> "NH2" Residue "I ARG 2061": "NH1" <-> "NH2" Residue "I ARG 2070": "NH1" <-> "NH2" Residue "I ARG 2088": "NH1" <-> "NH2" Residue "I ARG 2094": "NH1" <-> "NH2" Residue "I ARG 2098": "NH1" <-> "NH2" Residue "I ARG 2104": "NH1" <-> "NH2" Residue "I ARG 2110": "NH1" <-> "NH2" Residue "I PHE 2114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 2119": "NH1" <-> "NH2" Residue "I TYR 2136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 2139": "OD1" <-> "OD2" Residue "I ARG 2151": "NH1" <-> "NH2" Residue "I ARG 2165": "NH1" <-> "NH2" Residue "I ARG 2170": "NH1" <-> "NH2" Residue "I ARG 2184": "NH1" <-> "NH2" Residue "J ARG 134": "NH1" <-> "NH2" Residue "J ARG 142": "NH1" <-> "NH2" Residue "J PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 147": "NH1" <-> "NH2" Residue "J ARG 151": "NH1" <-> "NH2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 157": "NH1" <-> "NH2" Residue "J ARG 158": "NH1" <-> "NH2" Residue "J ARG 165": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J ARG 185": "NH1" <-> "NH2" Residue "J ARG 192": "NH1" <-> "NH2" Residue "J ARG 205": "NH1" <-> "NH2" Residue "J TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "J ARG 289": "NH1" <-> "NH2" Residue "J ARG 297": "NH1" <-> "NH2" Residue "J ARG 302": "NH1" <-> "NH2" Residue "J ARG 314": "NH1" <-> "NH2" Residue "J PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 36": "NH1" <-> "NH2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 134": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Residue "K PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 162": "NH1" <-> "NH2" Residue "K ARG 172": "NH1" <-> "NH2" Residue "K ARG 191": "NH1" <-> "NH2" Residue "K TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 218": "NH1" <-> "NH2" Residue "K TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 252": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 274": "NH1" <-> "NH2" Residue "K PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 330": "NH1" <-> "NH2" Residue "K ARG 332": "NH1" <-> "NH2" Residue "K ARG 338": "NH1" <-> "NH2" Residue "K ARG 379": "NH1" <-> "NH2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 16": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L ARG 134": "NH1" <-> "NH2" Residue "L TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 117": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "M ARG 123": "NH1" <-> "NH2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 202": "NH1" <-> "NH2" Residue "M ARG 205": "NH1" <-> "NH2" Residue "M TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 249": "NH1" <-> "NH2" Residue "M ARG 276": "NH1" <-> "NH2" Residue "M ARG 317": "NH1" <-> "NH2" Residue "M ARG 333": "NH1" <-> "NH2" Residue "M ARG 339": "NH1" <-> "NH2" Residue "M ARG 357": "NH1" <-> "NH2" Residue "M ARG 362": "NH1" <-> "NH2" Residue "M ARG 378": "NH1" <-> "NH2" Residue "M ARG 404": "NH1" <-> "NH2" Residue "M PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "N ARG 125": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 149": "NH1" <-> "NH2" Residue "N ARG 207": "NH1" <-> "NH2" Residue "N ARG 235": "NH1" <-> "NH2" Residue "N ARG 253": "NH1" <-> "NH2" Residue "N ARG 273": "NH1" <-> "NH2" Residue "N ARG 284": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "N ARG 330": "NH1" <-> "NH2" Residue "N ARG 334": "NH1" <-> "NH2" Residue "N ARG 336": "NH1" <-> "NH2" Residue "N ARG 353": "NH1" <-> "NH2" Residue "N ARG 372": "NH1" <-> "NH2" Residue "N ARG 374": "NH1" <-> "NH2" Residue "N ARG 392": "NH1" <-> "NH2" Residue "N ARG 400": "NH1" <-> "NH2" Residue "N ARG 414": "NH1" <-> "NH2" Residue "N ARG 416": "NH1" <-> "NH2" Residue "N ARG 428": "NH1" <-> "NH2" Residue "N ARG 438": "NH1" <-> "NH2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 117": "NH1" <-> "NH2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O ARG 123": "NH1" <-> "NH2" Residue "O ARG 184": "NH1" <-> "NH2" Residue "O ARG 202": "NH1" <-> "NH2" Residue "O ARG 205": "NH1" <-> "NH2" Residue "O ARG 249": "NH1" <-> "NH2" Residue "O ARG 276": "NH1" <-> "NH2" Residue "O ARG 317": "NH1" <-> "NH2" Residue "O ARG 333": "NH1" <-> "NH2" Residue "O ARG 339": "NH1" <-> "NH2" Residue "O ARG 357": "NH1" <-> "NH2" Residue "O ARG 362": "NH1" <-> "NH2" Residue "O ARG 378": "NH1" <-> "NH2" Residue "O ARG 404": "NH1" <-> "NH2" Residue "O TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 29": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 64": "NH1" <-> "NH2" Residue "P ARG 71": "NH1" <-> "NH2" Residue "P PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P ARG 130": "NH1" <-> "NH2" Residue "P ARG 149": "NH1" <-> "NH2" Residue "P ARG 207": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ASP 248": "OD1" <-> "OD2" Residue "P ARG 253": "NH1" <-> "NH2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 273": "NH1" <-> "NH2" Residue "P GLU 274": "OE1" <-> "OE2" Residue "P ARG 284": "NH1" <-> "NH2" Residue "P ARG 314": "NH1" <-> "NH2" Residue "P ARG 330": "NH1" <-> "NH2" Residue "P ARG 334": "NH1" <-> "NH2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "P ARG 353": "NH1" <-> "NH2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "P ARG 374": "NH1" <-> "NH2" Residue "P ARG 392": "NH1" <-> "NH2" Residue "P ARG 400": "NH1" <-> "NH2" Residue "P ARG 414": "NH1" <-> "NH2" Residue "P ARG 416": "NH1" <-> "NH2" Residue "P ARG 428": "NH1" <-> "NH2" Residue "P ARG 438": "NH1" <-> "NH2" Residue "P TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 14": "NH1" <-> "NH2" Residue "Q ARG 46": "NH1" <-> "NH2" Residue "Q ARG 64": "NH1" <-> "NH2" Residue "Q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 118": "NH1" <-> "NH2" Residue "Q ARG 123": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "Q TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 202": "NH1" <-> "NH2" Residue "Q ARG 205": "NH1" <-> "NH2" Residue "Q TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 249": "NH1" <-> "NH2" Residue "Q ARG 276": "NH1" <-> "NH2" Residue "Q ARG 317": "NH1" <-> "NH2" Residue "Q ARG 333": "NH1" <-> "NH2" Residue "Q ARG 339": "NH1" <-> "NH2" Residue "Q ARG 357": "NH1" <-> "NH2" Residue "Q ARG 362": "NH1" <-> "NH2" Residue "Q ARG 378": "NH1" <-> "NH2" Residue "Q ARG 404": "NH1" <-> "NH2" Residue "Q PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 29": "NH1" <-> "NH2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 71": "NH1" <-> "NH2" Residue "R ARG 124": "NH1" <-> "NH2" Residue "R ARG 125": "NH1" <-> "NH2" Residue "R ARG 130": "NH1" <-> "NH2" Residue "R ARG 207": "NH1" <-> "NH2" Residue "R PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 211": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "R PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 235": "NH1" <-> "NH2" Residue "R ARG 253": "NH1" <-> "NH2" Residue "R PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 273": "NH1" <-> "NH2" Residue "R ARG 284": "NH1" <-> "NH2" Residue "R ARG 314": "NH1" <-> "NH2" Residue "R ARG 330": "NH1" <-> "NH2" Residue "R ARG 334": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 353": "NH1" <-> "NH2" Residue "R ARG 372": "NH1" <-> "NH2" Residue "R ARG 374": "NH1" <-> "NH2" Residue "R ARG 392": "NH1" <-> "NH2" Residue "R ARG 400": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R ARG 416": "NH1" <-> "NH2" Residue "R ARG 428": "NH1" <-> "NH2" Residue "R ARG 438": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 37": "NH1" <-> "NH2" Residue "S ARG 39": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 116": "NH1" <-> "NH2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 177": "NH1" <-> "NH2" Residue "S ARG 183": "NH1" <-> "NH2" Residue "S ARG 196": "NH1" <-> "NH2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S ARG 210": "NH1" <-> "NH2" Residue "S TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 254": "NH1" <-> "NH2" Residue "S ARG 256": "NH1" <-> "NH2" Residue "S ARG 290": "NH1" <-> "NH2" Residue "S ARG 312": "NH1" <-> "NH2" Residue "S ARG 335": "NH1" <-> "NH2" Residue "S ARG 372": "NH1" <-> "NH2" Residue "T ARG 24": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "T ARG 79": "NH1" <-> "NH2" Residue "T PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 133": "NH1" <-> "NH2" Residue "T TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 164": "NH1" <-> "NH2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 230": "NH1" <-> "NH2" Residue "T ARG 239": "NH1" <-> "NH2" Residue "T ARG 248": "NH1" <-> "NH2" Residue "T PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 301": "NH1" <-> "NH2" Residue "T ARG 341": "NH1" <-> "NH2" Residue "T ARG 363": "NH1" <-> "NH2" Residue "T ARG 366": "NH1" <-> "NH2" Residue "T ARG 377": "NH1" <-> "NH2" Residue "T ARG 389": "NH1" <-> "NH2" Residue "T ARG 390": "NH1" <-> "NH2" Residue "T ARG 426": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 37": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U ARG 116": "NH1" <-> "NH2" Residue "U ARG 147": "NH1" <-> "NH2" Residue "U ARG 177": "NH1" <-> "NH2" Residue "U ARG 183": "NH1" <-> "NH2" Residue "U ARG 196": "NH1" <-> "NH2" Residue "U PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 206": "NH1" <-> "NH2" Residue "U ARG 210": "NH1" <-> "NH2" Residue "U TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U ARG 256": "NH1" <-> "NH2" Residue "U ARG 290": "NH1" <-> "NH2" Residue "U ARG 312": "NH1" <-> "NH2" Residue "U ARG 335": "NH1" <-> "NH2" Residue "V ARG 93": "NH1" <-> "NH2" Residue "V ARG 105": "NH1" <-> "NH2" Residue "V ARG 115": "NH1" <-> "NH2" Residue "V ARG 116": "NH1" <-> "NH2" Residue "V ARG 128": "NH1" <-> "NH2" Residue "V ARG 165": "NH1" <-> "NH2" Residue "V ARG 166": "NH1" <-> "NH2" Residue "V ARG 170": "NH1" <-> "NH2" Residue "V ARG 177": "NH1" <-> "NH2" Residue "V ARG 186": "NH1" <-> "NH2" Residue "V ARG 194": "NH1" <-> "NH2" Residue "V ARG 206": "NH1" <-> "NH2" Residue "V ARG 224": "NH1" <-> "NH2" Residue "V ARG 225": "NH1" <-> "NH2" Residue "V ARG 226": "NH1" <-> "NH2" Residue "V ARG 232": "NH1" <-> "NH2" Residue "V ARG 236": "NH1" <-> "NH2" Residue "V ARG 252": "NH1" <-> "NH2" Residue "V ARG 257": "NH1" <-> "NH2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 171": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 55488 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "I" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6519 Classifications: {'peptide': 792} Link IDs: {'PTRANS': 48, 'TRANS': 743} Chain breaks: 4 Chain: "J" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1316 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 13, 'TRANS': 144} Chain breaks: 1 Chain: "K" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3209 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain breaks: 1 Chain: "M" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3213 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3185 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "O" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3287 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3368 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 422} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3293 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "T" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3146 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 1 Chain: "U" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2802 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1617 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "W" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1542 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 178} Chain: "X" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2829 Classifications: {'DNA': 137} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 136} Chain: "Y" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2785 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.01, per 1000 atoms: 0.38 Number of scatterers: 55488 At special positions: 0 Unit cell: (204.102, 184.092, 229.448, 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 252 16.00 P 291 15.00 O 11015 8.00 N 9849 7.00 C 34081 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 Atom "ATOM 54662 O4' DT Y -29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54763 O4' DG Y -24 .*. O " rejected from bonding due to valence issues. Atom "HETATM55313 O3A ADP N 501 .*. O " rejected from bonding due to valence issues. Atom "ATOM 53097 O5' DG Y-106 .*. O " rejected from bonding due to valence issues. Atom "HETATM55316 O5' ADP N 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.14 Conformation dependent library (CDL) restraints added in 7.2 seconds 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 271 helices and 45 sheets defined 44.4% alpha, 10.7% beta 111 base pairs and 217 stacking pairs defined. Time for finding SS restraints: 18.35 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 46 through 74 removed outlier: 4.044A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.539A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 80 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.749A pdb=" N LYS B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 86 through 114 removed outlier: 3.596A pdb=" N LEU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 31 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.652A pdb=" N ALA D 76 " --> pdb=" O TYR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 45 through 73 removed outlier: 4.479A pdb=" N VAL E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 53 through 80 Processing helix chain 'F' and resid 88 through 96 Processing helix chain 'F' and resid 102 through 119 Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 64 through 77 removed outlier: 3.577A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 114 removed outlier: 3.562A pdb=" N MET G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 31 through 41 Processing helix chain 'H' and resid 50 through 76 Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'I' and resid 95 through 116 Processing helix chain 'I' and resid 137 through 250 removed outlier: 3.531A pdb=" N ALA I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER I 250 " --> pdb=" O LEU I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 634 Processing helix chain 'I' and resid 649 through 662 Processing helix chain 'I' and resid 679 through 689 Processing helix chain 'I' and resid 702 through 709 Processing helix chain 'I' and resid 725 through 730 Processing helix chain 'I' and resid 732 through 736 Processing helix chain 'I' and resid 748 through 751 Processing helix chain 'I' and resid 757 through 763 Processing helix chain 'I' and resid 782 through 791 Processing helix chain 'I' and resid 865 through 874 Processing helix chain 'I' and resid 876 through 883 Processing helix chain 'I' and resid 887 through 900 Processing helix chain 'I' and resid 904 through 906 No H-bonds generated for 'chain 'I' and resid 904 through 906' Processing helix chain 'I' and resid 937 through 939 No H-bonds generated for 'chain 'I' and resid 937 through 939' Processing helix chain 'I' and resid 943 through 946 Processing helix chain 'I' and resid 949 through 951 No H-bonds generated for 'chain 'I' and resid 949 through 951' Processing helix chain 'I' and resid 957 through 961 Processing helix chain 'I' and resid 964 through 967 No H-bonds generated for 'chain 'I' and resid 964 through 967' Processing helix chain 'I' and resid 971 through 977 Processing helix chain 'I' and resid 1887 through 1912 removed outlier: 3.943A pdb=" N GLY I1912 " --> pdb=" O SER I1908 " (cutoff:3.500A) Processing helix chain 'I' and resid 1920 through 1926 Processing helix chain 'I' and resid 1946 through 1949 No H-bonds generated for 'chain 'I' and resid 1946 through 1949' Processing helix chain 'I' and resid 1953 through 1958 removed outlier: 3.771A pdb=" N ALA I1958 " --> pdb=" O ALA I1954 " (cutoff:3.500A) Processing helix chain 'I' and resid 1962 through 1976 removed outlier: 4.781A pdb=" N GLU I1971 " --> pdb=" O ASP I1967 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE I1972 " --> pdb=" O GLN I1968 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG I1975 " --> pdb=" O GLU I1971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1998 through 2013 removed outlier: 4.121A pdb=" N ARG I2002 " --> pdb=" O TRP I1998 " (cutoff:3.500A) Processing helix chain 'I' and resid 2015 through 2029 removed outlier: 3.700A pdb=" N ARG I2019 " --> pdb=" O PRO I2016 " (cutoff:3.500A) Proline residue: I2020 - end of helix Processing helix chain 'I' and resid 2043 through 2056 Processing helix chain 'I' and resid 2069 through 2079 Processing helix chain 'I' and resid 2095 through 2104 Processing helix chain 'I' and resid 2145 through 2152 Processing helix chain 'I' and resid 2173 through 2189 Processing helix chain 'J' and resid 139 through 158 removed outlier: 4.160A pdb=" N THR J 144 " --> pdb=" O HIS J 140 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN J 152 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY J 153 " --> pdb=" O GLN J 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG J 158 " --> pdb=" O GLN J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 198 removed outlier: 4.135A pdb=" N LEU J 182 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 275 No H-bonds generated for 'chain 'J' and resid 272 through 275' Processing helix chain 'J' and resid 313 through 329 removed outlier: 4.359A pdb=" N LYS J 317 " --> pdb=" O ALA J 313 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 47 Processing helix chain 'K' and resid 68 through 79 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 177 through 192 Processing helix chain 'K' and resid 200 through 209 removed outlier: 3.764A pdb=" N GLU K 207 " --> pdb=" O ASN K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 224 Processing helix chain 'K' and resid 272 through 276 Processing helix chain 'K' and resid 278 through 280 No H-bonds generated for 'chain 'K' and resid 278 through 280' Processing helix chain 'K' and resid 295 through 300 Processing helix chain 'K' and resid 307 through 315 Proline residue: K 311 - end of helix Processing helix chain 'K' and resid 323 through 325 No H-bonds generated for 'chain 'K' and resid 323 through 325' Processing helix chain 'K' and resid 329 through 340 Processing helix chain 'K' and resid 358 through 368 removed outlier: 4.776A pdb=" N GLU K 368 " --> pdb=" O LYS K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 375 No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 379 through 385 Processing helix chain 'K' and resid 388 through 392 Processing helix chain 'L' and resid 21 through 36 Processing helix chain 'L' and resid 84 through 94 removed outlier: 4.152A pdb=" N SER L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 104 No H-bonds generated for 'chain 'L' and resid 101 through 104' Processing helix chain 'L' and resid 138 through 147 Processing helix chain 'M' and resid 43 through 58 removed outlier: 3.657A pdb=" N LEU M 55 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 87 Processing helix chain 'M' and resid 98 through 101 Processing helix chain 'M' and resid 108 through 119 Processing helix chain 'M' and resid 174 through 183 removed outlier: 3.601A pdb=" N GLU M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 248 removed outlier: 3.919A pdb=" N ASP M 244 " --> pdb=" O LEU M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 276 through 289 Processing helix chain 'M' and resid 304 through 306 No H-bonds generated for 'chain 'M' and resid 304 through 306' Processing helix chain 'M' and resid 309 through 320 removed outlier: 4.302A pdb=" N GLU M 320 " --> pdb=" O HIS M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 349 No H-bonds generated for 'chain 'M' and resid 347 through 349' Processing helix chain 'M' and resid 352 through 355 No H-bonds generated for 'chain 'M' and resid 352 through 355' Processing helix chain 'M' and resid 368 through 382 Processing helix chain 'M' and resid 388 through 400 Processing helix chain 'M' and resid 403 through 420 removed outlier: 3.920A pdb=" N LEU M 410 " --> pdb=" O SER M 406 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR M 411 " --> pdb=" O VAL M 407 " (cutoff:3.500A) Proline residue: M 412 - end of helix Processing helix chain 'M' and resid 427 through 436 removed outlier: 3.654A pdb=" N GLU M 431 " --> pdb=" O LYS M 427 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU M 432 " --> pdb=" O GLU M 428 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 442 through 449 removed outlier: 4.662A pdb=" N ASP M 449 " --> pdb=" O LYS M 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 65 removed outlier: 3.508A pdb=" N VAL N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 94 removed outlier: 3.776A pdb=" N ALA N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 125 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 244 through 251 Processing helix chain 'N' and resid 272 through 283 Processing helix chain 'N' and resid 301 through 303 No H-bonds generated for 'chain 'N' and resid 301 through 303' Processing helix chain 'N' and resid 306 through 317 removed outlier: 3.855A pdb=" N ARG N 314 " --> pdb=" O SER N 310 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU N 317 " --> pdb=" O ASN N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 345 No H-bonds generated for 'chain 'N' and resid 343 through 345' Processing helix chain 'N' and resid 348 through 353 removed outlier: 4.110A pdb=" N ARG N 353 " --> pdb=" O ASP N 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 377 Processing helix chain 'N' and resid 384 through 396 Processing helix chain 'N' and resid 399 through 413 removed outlier: 4.444A pdb=" N THR N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA N 408 " --> pdb=" O GLN N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 432 Processing helix chain 'N' and resid 436 through 441 removed outlier: 3.656A pdb=" N GLN N 441 " --> pdb=" O SER N 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 58 removed outlier: 3.669A pdb=" N VAL O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 98 through 101 Processing helix chain 'O' and resid 108 through 118 removed outlier: 3.500A pdb=" N LEU O 112 " --> pdb=" O LYS O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 183 Processing helix chain 'O' and resid 207 through 212 removed outlier: 4.286A pdb=" N THR O 211 " --> pdb=" O THR O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 248 Processing helix chain 'O' and resid 257 through 261 Processing helix chain 'O' and resid 272 through 275 No H-bonds generated for 'chain 'O' and resid 272 through 275' Processing helix chain 'O' and resid 278 through 287 Processing helix chain 'O' and resid 304 through 306 No H-bonds generated for 'chain 'O' and resid 304 through 306' Processing helix chain 'O' and resid 309 through 320 removed outlier: 3.601A pdb=" N HIS O 316 " --> pdb=" O PHE O 312 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 349 No H-bonds generated for 'chain 'O' and resid 347 through 349' Processing helix chain 'O' and resid 352 through 357 removed outlier: 4.235A pdb=" N ARG O 357 " --> pdb=" O ASP O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 381 Processing helix chain 'O' and resid 388 through 400 Processing helix chain 'O' and resid 403 through 420 removed outlier: 4.283A pdb=" N LEU O 410 " --> pdb=" O SER O 406 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR O 411 " --> pdb=" O VAL O 407 " (cutoff:3.500A) Proline residue: O 412 - end of helix Processing helix chain 'O' and resid 427 through 436 Processing helix chain 'O' and resid 440 through 449 Processing helix chain 'O' and resid 451 through 453 No H-bonds generated for 'chain 'O' and resid 451 through 453' Processing helix chain 'P' and resid 50 through 65 Processing helix chain 'P' and resid 83 through 94 Processing helix chain 'P' and resid 105 through 107 No H-bonds generated for 'chain 'P' and resid 105 through 107' Processing helix chain 'P' and resid 115 through 126 removed outlier: 3.790A pdb=" N SER P 126 " --> pdb=" O ALA P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 185 Processing helix chain 'P' and resid 209 through 211 No H-bonds generated for 'chain 'P' and resid 209 through 211' Processing helix chain 'P' and resid 244 through 252 Processing helix chain 'P' and resid 258 through 261 No H-bonds generated for 'chain 'P' and resid 258 through 261' Processing helix chain 'P' and resid 271 through 286 Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 306 through 317 removed outlier: 4.114A pdb=" N ARG P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU P 317 " --> pdb=" O ASN P 313 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 345 No H-bonds generated for 'chain 'P' and resid 343 through 345' Processing helix chain 'P' and resid 348 through 351 No H-bonds generated for 'chain 'P' and resid 348 through 351' Processing helix chain 'P' and resid 364 through 377 Processing helix chain 'P' and resid 384 through 396 Processing helix chain 'P' and resid 399 through 415 removed outlier: 3.698A pdb=" N ILE P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR P 407 " --> pdb=" O ILE P 403 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA P 408 " --> pdb=" O GLN P 404 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL P 412 " --> pdb=" O ALA P 408 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 432 Processing helix chain 'P' and resid 436 through 442 Processing helix chain 'Q' and resid 36 through 38 No H-bonds generated for 'chain 'Q' and resid 36 through 38' Processing helix chain 'Q' and resid 43 through 57 removed outlier: 3.605A pdb=" N ALA Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 87 removed outlier: 4.006A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 108 through 119 Processing helix chain 'Q' and resid 174 through 183 Processing helix chain 'Q' and resid 207 through 209 No H-bonds generated for 'chain 'Q' and resid 207 through 209' Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 259 through 262 removed outlier: 4.026A pdb=" N GLN Q 262 " --> pdb=" O MET Q 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 259 through 262' Processing helix chain 'Q' and resid 272 through 277 Processing helix chain 'Q' and resid 279 through 289 Processing helix chain 'Q' and resid 304 through 306 No H-bonds generated for 'chain 'Q' and resid 304 through 306' Processing helix chain 'Q' and resid 309 through 318 Processing helix chain 'Q' and resid 347 through 349 No H-bonds generated for 'chain 'Q' and resid 347 through 349' Processing helix chain 'Q' and resid 352 through 357 removed outlier: 3.898A pdb=" N ARG Q 357 " --> pdb=" O ASP Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 381 Processing helix chain 'Q' and resid 388 through 400 removed outlier: 3.536A pdb=" N LYS Q 400 " --> pdb=" O GLU Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 403 through 408 Processing helix chain 'Q' and resid 411 through 419 Processing helix chain 'Q' and resid 427 through 436 Processing helix chain 'Q' and resid 440 through 449 Processing helix chain 'R' and resid 50 through 65 Processing helix chain 'R' and resid 83 through 93 Processing helix chain 'R' and resid 117 through 126 Processing helix chain 'R' and resid 176 through 185 Processing helix chain 'R' and resid 213 through 215 No H-bonds generated for 'chain 'R' and resid 213 through 215' Processing helix chain 'R' and resid 244 through 249 removed outlier: 4.192A pdb=" N ILE R 247 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 259 removed outlier: 3.572A pdb=" N ALA R 259 " --> pdb=" O GLN R 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 255 through 259' Processing helix chain 'R' and resid 269 through 272 No H-bonds generated for 'chain 'R' and resid 269 through 272' Processing helix chain 'R' and resid 275 through 286 Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 306 through 317 removed outlier: 3.905A pdb=" N ARG R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 345 No H-bonds generated for 'chain 'R' and resid 343 through 345' Processing helix chain 'R' and resid 348 through 353 removed outlier: 4.380A pdb=" N ARG R 353 " --> pdb=" O ASP R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 378 removed outlier: 3.797A pdb=" N LYS R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU R 378 " --> pdb=" O ARG R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 394 Processing helix chain 'R' and resid 399 through 415 removed outlier: 3.883A pdb=" N THR R 407 " --> pdb=" O ILE R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 432 Processing helix chain 'R' and resid 436 through 442 Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.951A pdb=" N SER S 60 " --> pdb=" O GLU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 91 Processing helix chain 'S' and resid 98 through 100 No H-bonds generated for 'chain 'S' and resid 98 through 100' Processing helix chain 'S' and resid 113 through 125 Processing helix chain 'S' and resid 137 through 145 Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 182 through 196 Processing helix chain 'S' and resid 203 through 216 removed outlier: 3.511A pdb=" N GLU S 207 " --> pdb=" O THR S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 223 through 232 Processing helix chain 'S' and resid 252 through 261 removed outlier: 4.418A pdb=" N CYS S 257 " --> pdb=" O ARG S 254 " (cutoff:3.500A) Proline residue: S 258 - end of helix Processing helix chain 'S' and resid 264 through 266 No H-bonds generated for 'chain 'S' and resid 264 through 266' Processing helix chain 'S' and resid 274 through 284 Processing helix chain 'S' and resid 287 through 295 removed outlier: 4.400A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 302 through 305 Processing helix chain 'S' and resid 309 through 320 Processing helix chain 'S' and resid 335 through 348 removed outlier: 5.313A pdb=" N VAL S 339 " --> pdb=" O LYS S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 354 removed outlier: 4.040A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 365 Processing helix chain 'S' and resid 367 through 373 Processing helix chain 'T' and resid 96 through 108 Processing helix chain 'T' and resid 115 through 117 No H-bonds generated for 'chain 'T' and resid 115 through 117' Processing helix chain 'T' and resid 130 through 142 Processing helix chain 'T' and resid 154 through 162 Processing helix chain 'T' and resid 189 through 191 No H-bonds generated for 'chain 'T' and resid 189 through 191' Processing helix chain 'T' and resid 199 through 213 Processing helix chain 'T' and resid 220 through 222 No H-bonds generated for 'chain 'T' and resid 220 through 222' Processing helix chain 'T' and resid 248 through 266 Processing helix chain 'T' and resid 276 through 281 removed outlier: 3.668A pdb=" N GLN T 281 " --> pdb=" O GLN T 277 " (cutoff:3.500A) Processing helix chain 'T' and resid 300 through 308 removed outlier: 3.676A pdb=" N ILE T 304 " --> pdb=" O GLU T 300 " (cutoff:3.500A) Proline residue: T 305 - end of helix removed outlier: 4.567A pdb=" N LEU T 308 " --> pdb=" O ILE T 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 300 through 308' Processing helix chain 'T' and resid 311 through 313 No H-bonds generated for 'chain 'T' and resid 311 through 313' Processing helix chain 'T' and resid 325 through 334 Processing helix chain 'T' and resid 338 through 346 Proline residue: T 342 - end of helix Processing helix chain 'T' and resid 354 through 356 No H-bonds generated for 'chain 'T' and resid 354 through 356' Processing helix chain 'T' and resid 360 through 371 Processing helix chain 'T' and resid 386 through 390 Processing helix chain 'T' and resid 392 through 401 Processing helix chain 'T' and resid 405 through 408 Processing helix chain 'T' and resid 413 through 419 Processing helix chain 'T' and resid 421 through 427 removed outlier: 3.717A pdb=" N VAL T 424 " --> pdb=" O LYS T 421 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 64 removed outlier: 5.956A pdb=" N GLY U 63 " --> pdb=" O GLN U 59 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 92 removed outlier: 4.292A pdb=" N TYR U 91 " --> pdb=" O HIS U 87 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN U 92 " --> pdb=" O HIS U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 127 Processing helix chain 'U' and resid 137 through 144 Processing helix chain 'U' and resid 166 through 168 No H-bonds generated for 'chain 'U' and resid 166 through 168' Processing helix chain 'U' and resid 172 through 174 No H-bonds generated for 'chain 'U' and resid 172 through 174' Processing helix chain 'U' and resid 183 through 196 removed outlier: 3.678A pdb=" N ASP U 187 " --> pdb=" O ARG U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 203 through 214 removed outlier: 5.683A pdb=" N ILE U 208 " --> pdb=" O ALA U 204 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL U 209 " --> pdb=" O GLU U 205 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS U 213 " --> pdb=" O VAL U 209 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU U 214 " --> pdb=" O ARG U 210 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 231 Processing helix chain 'U' and resid 259 through 261 No H-bonds generated for 'chain 'U' and resid 259 through 261' Processing helix chain 'U' and resid 264 through 266 No H-bonds generated for 'chain 'U' and resid 264 through 266' Processing helix chain 'U' and resid 274 through 284 Processing helix chain 'U' and resid 287 through 295 removed outlier: 3.991A pdb=" N LYS U 291 " --> pdb=" O VAL U 287 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP U 292 " --> pdb=" O ASP U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 305 Processing helix chain 'U' and resid 308 through 320 Processing helix chain 'U' and resid 335 through 347 removed outlier: 5.592A pdb=" N VAL U 339 " --> pdb=" O LYS U 336 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 355 No H-bonds generated for 'chain 'U' and resid 353 through 355' Processing helix chain 'U' and resid 359 through 368 removed outlier: 4.092A pdb=" N GLU U 364 " --> pdb=" O GLN U 360 " (cutoff:3.500A) Proline residue: U 367 - end of helix Processing helix chain 'V' and resid 55 through 62 Processing helix chain 'V' and resid 125 through 128 removed outlier: 3.875A pdb=" N ARG V 128 " --> pdb=" O PRO V 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 125 through 128' Processing helix chain 'V' and resid 140 through 145 Processing helix chain 'V' and resid 154 through 166 removed outlier: 3.756A pdb=" N HIS V 159 " --> pdb=" O ALA V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 177 removed outlier: 3.947A pdb=" N ASP V 176 " --> pdb=" O VAL V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 203 removed outlier: 3.579A pdb=" N ALA V 203 " --> pdb=" O CYS V 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 221 through 234 removed outlier: 3.516A pdb=" N ARG V 225 " --> pdb=" O GLY V 221 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU V 230 " --> pdb=" O ARG V 226 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU V 233 " --> pdb=" O GLN V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 257 Processing helix chain 'W' and resid 59 through 61 No H-bonds generated for 'chain 'W' and resid 59 through 61' Processing helix chain 'W' and resid 124 through 128 Processing helix chain 'W' and resid 149 through 156 Processing helix chain 'W' and resid 172 through 203 removed outlier: 3.780A pdb=" N LYS W 182 " --> pdb=" O LYS W 178 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 639 through 641 removed outlier: 6.519A pdb=" N LEU I 671 " --> pdb=" O ILE I 744 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASP I 746 " --> pdb=" O LEU I 671 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE I 673 " --> pdb=" O ASP I 746 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS I 721 " --> pdb=" O ILE I 672 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 857 through 859 removed outlier: 3.541A pdb=" N ILE I2167 " --> pdb=" O ILE I 857 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 916 through 918 Processing sheet with id= D, first strand: chain 'I' and resid 2062 through 2065 Processing sheet with id= E, first strand: chain 'I' and resid 2133 through 2135 Processing sheet with id= F, first strand: chain 'K' and resid 92 through 95 Processing sheet with id= G, first strand: chain 'K' and resid 29 through 31 Processing sheet with id= H, first strand: chain 'K' and resid 317 through 321 removed outlier: 8.134A pdb=" N VAL K 318 " --> pdb=" O CYS K 144 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE K 146 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR K 320 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL K 148 " --> pdb=" O THR K 320 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 358 through 363 removed outlier: 7.000A pdb=" N ALA M 65 " --> pdb=" O MET M 359 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE M 361 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU M 67 " --> pdb=" O ILE M 361 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR M 363 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA M 69 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL M 327 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU M 68 " --> pdb=" O VAL M 327 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE M 329 " --> pdb=" O LEU M 68 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY M 70 " --> pdb=" O PHE M 329 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER M 331 " --> pdb=" O GLY M 70 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 237 through 239 removed outlier: 3.624A pdb=" N VAL M 295 " --> pdb=" O GLY M 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 229 through 231 removed outlier: 3.530A pdb=" N GLY M 204 " --> pdb=" O VAL M 190 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR M 192 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG M 202 " --> pdb=" O TYR M 192 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'M' and resid 166 through 172 removed outlier: 4.032A pdb=" N GLU M 137 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS M 162 " --> pdb=" O VAL M 135 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL M 135 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 355 through 359 removed outlier: 6.738A pdb=" N LEU N 324 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE N 75 " --> pdb=" O LEU N 324 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET N 326 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLY N 77 " --> pdb=" O MET N 326 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 289 through 293 Processing sheet with id= O, first strand: chain 'N' and resid 192 through 196 removed outlier: 6.609A pdb=" N THR N 162 " --> pdb=" O VAL N 143 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE N 145 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS N 160 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE N 147 " --> pdb=" O VAL N 158 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL N 158 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY N 159 " --> pdb=" O LEU N 174 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 332 through 334 Processing sheet with id= Q, first strand: chain 'O' and resid 359 through 362 removed outlier: 6.429A pdb=" N VAL O 327 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU O 68 " --> pdb=" O VAL O 327 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE O 329 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 292 through 296 Processing sheet with id= S, first strand: chain 'O' and resid 130 through 134 removed outlier: 3.813A pdb=" N GLY O 133 " --> pdb=" O ILE O 191 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE O 191 " --> pdb=" O GLY O 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY O 204 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR O 192 " --> pdb=" O ARG O 202 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG O 202 " --> pdb=" O TYR O 192 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU O 194 " --> pdb=" O VAL O 200 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL O 200 " --> pdb=" O GLU O 194 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 167 through 172 removed outlier: 6.770A pdb=" N CYS O 141 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL O 157 " --> pdb=" O THR O 139 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR O 139 " --> pdb=" O VAL O 157 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 335 through 337 removed outlier: 3.737A pdb=" N CYS O 336 " --> pdb=" O SER O 346 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 354 through 359 removed outlier: 7.273A pdb=" N ALA P 72 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL P 357 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU P 74 " --> pdb=" O VAL P 357 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR P 359 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA P 76 " --> pdb=" O THR P 359 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU P 324 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE P 75 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET P 326 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY P 77 " --> pdb=" O MET P 326 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR P 328 " --> pdb=" O GLY P 77 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 128 through 133 Processing sheet with id= X, first strand: chain 'P' and resid 169 through 174 removed outlier: 4.025A pdb=" N GLY P 159 " --> pdb=" O LEU P 174 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU P 144 " --> pdb=" O THR P 162 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS P 164 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL P 142 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP P 191 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY P 206 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR P 194 " --> pdb=" O LYS P 204 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS P 204 " --> pdb=" O THR P 194 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP P 196 " --> pdb=" O ILE P 202 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE P 202 " --> pdb=" O ASP P 196 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 332 through 334 Processing sheet with id= Z, first strand: chain 'Q' and resid 359 through 363 removed outlier: 6.516A pdb=" N VAL Q 327 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU Q 68 " --> pdb=" O VAL Q 327 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE Q 329 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY Q 70 " --> pdb=" O PHE Q 329 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER Q 331 " --> pdb=" O GLY Q 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP Q 302 " --> pdb=" O MET Q 96 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 229 through 239 removed outlier: 3.801A pdb=" N LYS Q 232 " --> pdb=" O LYS Q 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS Q 128 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 167 through 172 removed outlier: 4.037A pdb=" N HIS Q 156 " --> pdb=" O CYS Q 141 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU Q 137 " --> pdb=" O GLY Q 160 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS Q 162 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL Q 135 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 335 through 337 Processing sheet with id= AD, first strand: chain 'Q' and resid 189 through 193 removed outlier: 3.588A pdb=" N GLY Q 204 " --> pdb=" O VAL Q 190 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR Q 192 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG Q 202 " --> pdb=" O TYR Q 192 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 355 through 358 removed outlier: 6.240A pdb=" N LEU R 324 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE R 75 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET R 326 " --> pdb=" O ILE R 75 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 289 through 293 Processing sheet with id= AG, first strand: chain 'R' and resid 192 through 196 removed outlier: 6.598A pdb=" N THR R 162 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE R 145 " --> pdb=" O LYS R 160 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS R 160 " --> pdb=" O ILE R 145 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE R 147 " --> pdb=" O VAL R 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL R 158 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY R 159 " --> pdb=" O LEU R 174 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'S' and resid 132 through 136 removed outlier: 6.306A pdb=" N VAL S 103 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA S 135 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU S 105 " --> pdb=" O ALA S 135 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU S 8 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR S 106 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL S 10 " --> pdb=" O THR S 106 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'S' and resid 35 through 38 Processing sheet with id= AJ, first strand: chain 'S' and resid 297 through 300 removed outlier: 6.144A pdb=" N ILE S 151 " --> pdb=" O VAL S 298 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER S 300 " --> pdb=" O ILE S 151 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N MET S 153 " --> pdb=" O SER S 300 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 238 through 241 Processing sheet with id= AL, first strand: chain 'T' and resid 35 through 38 removed outlier: 7.541A pdb=" N PHE T 16 " --> pdb=" O PRO T 119 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU T 121 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE T 18 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER T 123 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 349 through 351 Processing sheet with id= AN, first strand: chain 'T' and resid 285 through 288 Processing sheet with id= AO, first strand: chain 'T' and resid 223 through 226 removed outlier: 6.671A pdb=" N LYS T 238 " --> pdb=" O ALA T 224 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'U' and resid 35 through 38 Processing sheet with id= AQ, first strand: chain 'V' and resid 96 through 101 Processing sheet with id= AR, first strand: chain 'W' and resid 133 through 145 Processing sheet with id= AS, first strand: chain 'W' and resid 78 through 81 removed outlier: 7.051A pdb=" N PHE W 103 " --> pdb=" O LYS W 64 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE W 66 " --> pdb=" O LYS W 101 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS W 101 " --> pdb=" O ILE W 66 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE W 68 " --> pdb=" O ILE W 99 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE W 99 " --> pdb=" O PHE W 68 " (cutoff:3.500A) 1986 hydrogen bonds defined for protein. 5661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 280 hydrogen bonds 560 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 217 stacking parallelities Total time for adding SS restraints: 21.99 Time building geometry restraints manager: 19.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9548 1.33 - 1.45: 15111 1.45 - 1.57: 31399 1.57 - 1.69: 574 1.69 - 1.81: 418 Bond restraints: 57050 Sorted by residual: bond pdb=" C4 ATP U 401 " pdb=" C5 ATP U 401 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.93e+01 bond pdb=" C4 ATP T 501 " pdb=" C5 ATP T 501 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.27e+01 bond pdb=" C5 ATP U 401 " pdb=" C6 ATP U 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.81e+01 bond pdb=" C4 ATP T 501 " pdb=" N9 ATP T 501 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" C5 ATP T 501 " pdb=" N7 ATP T 501 " ideal model delta sigma weight residual 1.387 1.335 0.052 1.00e-02 1.00e+04 2.65e+01 ... (remaining 57045 not shown) Histogram of bond angle deviations from ideal: 91.89 - 101.01: 140 101.01 - 110.13: 12811 110.13 - 119.25: 36331 119.25 - 128.37: 28224 128.37 - 137.50: 737 Bond angle restraints: 78243 Sorted by residual: angle pdb=" PB ATP U 401 " pdb=" O3B ATP U 401 " pdb=" PG ATP U 401 " ideal model delta sigma weight residual 139.87 113.82 26.05 1.00e+00 1.00e+00 6.79e+02 angle pdb=" PA ATP U 401 " pdb=" O3A ATP U 401 " pdb=" PB ATP U 401 " ideal model delta sigma weight residual 136.83 113.16 23.67 1.00e+00 1.00e+00 5.60e+02 angle pdb=" PB ATP T 501 " pdb=" O3B ATP T 501 " pdb=" PG ATP T 501 " ideal model delta sigma weight residual 139.87 116.37 23.50 1.00e+00 1.00e+00 5.52e+02 angle pdb=" PA ATP T 501 " pdb=" O3A ATP T 501 " pdb=" PB ATP T 501 " ideal model delta sigma weight residual 136.83 114.34 22.49 1.00e+00 1.00e+00 5.06e+02 angle pdb=" CA PRO J 283 " pdb=" N PRO J 283 " pdb=" CD PRO J 283 " ideal model delta sigma weight residual 112.00 99.68 12.32 1.40e+00 5.10e-01 7.75e+01 ... (remaining 78238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 32288 34.65 - 69.31: 1785 69.31 - 103.96: 55 103.96 - 138.62: 6 138.62 - 173.27: 1 Dihedral angle restraints: 34135 sinusoidal: 15960 harmonic: 18175 Sorted by residual: dihedral pdb=" CA THR W 170 " pdb=" C THR W 170 " pdb=" N GLU W 171 " pdb=" CA GLU W 171 " ideal model delta harmonic sigma weight residual -180.00 -62.91 -117.09 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA CYS U 257 " pdb=" C CYS U 257 " pdb=" N PRO U 258 " pdb=" CA PRO U 258 " ideal model delta harmonic sigma weight residual 180.00 130.78 49.22 0 5.00e+00 4.00e-02 9.69e+01 dihedral pdb=" CD ARG I 163 " pdb=" NE ARG I 163 " pdb=" CZ ARG I 163 " pdb=" NH1 ARG I 163 " ideal model delta sinusoidal sigma weight residual 0.00 89.01 -89.01 1 1.00e+01 1.00e-02 9.43e+01 ... (remaining 34132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 8813 0.321 - 0.642: 13 0.642 - 0.962: 0 0.962 - 1.283: 0 1.283 - 1.604: 1 Chirality restraints: 8827 Sorted by residual: chirality pdb=" CB ILE M 234 " pdb=" CA ILE M 234 " pdb=" CG1 ILE M 234 " pdb=" CG2 ILE M 234 " both_signs ideal model delta sigma weight residual False 2.64 1.04 1.60 2.00e-01 2.50e+01 6.43e+01 chirality pdb=" P DT Y -4 " pdb=" OP1 DT Y -4 " pdb=" OP2 DT Y -4 " pdb=" O5' DT Y -4 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" P DA X 4 " pdb=" OP1 DA X 4 " pdb=" OP2 DA X 4 " pdb=" O5' DA X 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 8824 not shown) Planarity restraints: 9069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 163 " -1.101 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG I 163 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG I 163 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 163 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG I 163 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 260 " -1.074 9.50e-02 1.11e+02 4.81e-01 1.40e+02 pdb=" NE ARG J 260 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG J 260 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 260 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 260 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 167 " 0.941 9.50e-02 1.11e+02 4.22e-01 1.08e+02 pdb=" NE ARG I 167 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG I 167 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 167 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 167 " 0.023 2.00e-02 2.50e+03 ... (remaining 9066 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 26 1.91 - 2.66: 1290 2.66 - 3.41: 79265 3.41 - 4.15: 138810 4.15 - 4.90: 242706 Nonbonded interactions: 462097 Sorted by model distance: nonbonded pdb=" NH2 ARG A 43 " pdb=" O3' DC Y -35 " model vdw 1.169 2.520 nonbonded pdb=" O THR M 74 " pdb=" O3B ADP M 501 " model vdw 1.294 3.040 nonbonded pdb=" NH1 ARG B 28 " pdb=" OP1 DA Y -22 " model vdw 1.311 2.520 nonbonded pdb=" CG ARG I 736 " pdb=" OP1 DG Y-130 " model vdw 1.314 3.440 nonbonded pdb=" CZ ARG A 43 " pdb=" O3' DC Y -35 " model vdw 1.372 3.270 ... (remaining 462092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 119) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 28 through 121) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 41 through 134) selection = (chain 'G' and resid 41 through 134) } ncs_group { reference = (chain 'D' and resid 23 through 102) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 15 through 451 or resid 501)) selection = (chain 'O' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) selection = (chain 'Q' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) } ncs_group { reference = (chain 'N' and (resid 18 through 148 or resid 157 through 447 or resid 501)) selection = (chain 'P' and (resid 18 through 148 or resid 157 through 208 or resid 225 throu \ gh 447 or resid 501)) selection = (chain 'R' and (resid 18 through 208 or resid 225 through 447 or resid 501)) } ncs_group { reference = (chain 'S' and (resid 2 through 40 or resid 52 through 371)) selection = (chain 'U' and resid 2 through 371) } 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=0.01 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: 2.340 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: 0.030 Extract box with map and model: 14.610 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 125.160 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4351 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 : 0.004 0.149 57050 Z= 0.230 Angle : 0.685 26.050 78243 Z= 0.439 Chirality : 0.047 1.604 8827 Planarity : 0.011 0.493 9069 Dihedral : 17.101 173.273 22401 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.58 % Favored : 95.21 % Rotamer: Outliers : 4.96 % Allowed : 5.79 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.03 % 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: -2.12 (0.10), residues: 6201 helix: -0.57 (0.09), residues: 2880 sheet: -1.86 (0.17), residues: 761 loop : -2.16 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 667 HIS 0.008 0.001 HIS M 316 PHE 0.016 0.001 PHE W 68 TYR 0.017 0.001 TYR V 246 ARG 0.006 0.000 ARG K 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1065 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.3824 (ptpt) cc_final: 0.3469 (mmtp) REVERT: F 30 ARG cc_start: -0.0803 (OUTLIER) cc_final: -0.1715 (mtp-110) REVERT: I 95 GLU cc_start: -0.0982 (OUTLIER) cc_final: -0.1625 (tt0) REVERT: I 99 GLN cc_start: -0.2431 (OUTLIER) cc_final: -0.2711 (mt0) REVERT: I 136 HIS cc_start: 0.0276 (OUTLIER) cc_final: -0.0417 (t-170) REVERT: I 789 MET cc_start: 0.2012 (ttp) cc_final: 0.1040 (ppp) REVERT: I 2060 HIS cc_start: 0.5510 (m-70) cc_final: 0.5182 (m170) REVERT: I 2185 MET cc_start: 0.4439 (mmm) cc_final: 0.4196 (tpp) REVERT: I 2189 MET cc_start: 0.3765 (mmm) cc_final: 0.3027 (ttm) REVERT: J 182 LEU cc_start: 0.4794 (mt) cc_final: 0.4376 (tt) REVERT: J 190 TYR cc_start: 0.3363 (t80) cc_final: 0.3116 (t80) REVERT: K 22 VAL cc_start: 0.6758 (t) cc_final: 0.6363 (m) REVERT: K 269 ARG cc_start: 0.4362 (OUTLIER) cc_final: 0.3060 (mmm-85) REVERT: K 309 MET cc_start: 0.7431 (mpt) cc_final: 0.7129 (mmt) REVERT: K 319 LEU cc_start: 0.7531 (mt) cc_final: 0.7163 (mt) REVERT: K 336 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: L 1 MET cc_start: 0.1117 (mtt) cc_final: 0.0417 (tpt) REVERT: L 37 ASN cc_start: 0.6038 (t0) cc_final: 0.5518 (p0) REVERT: L 153 THR cc_start: 0.1966 (p) cc_final: 0.1747 (p) REVERT: M 236 GLN cc_start: 0.6500 (tt0) cc_final: 0.6145 (mt0) REVERT: M 323 ILE cc_start: 0.8669 (pp) cc_final: 0.8392 (mp) REVERT: M 363 THR cc_start: 0.8321 (m) cc_final: 0.7801 (p) REVERT: M 414 ASN cc_start: 0.6762 (t0) cc_final: 0.6550 (t0) REVERT: N 120 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.6846 (t) REVERT: N 133 GLU cc_start: 0.6719 (tp30) cc_final: 0.6110 (tp30) REVERT: N 372 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6945 (mtt90) REVERT: N 389 VAL cc_start: 0.7275 (t) cc_final: 0.6943 (p) REVERT: O 64 ARG cc_start: 0.7014 (mmt-90) cc_final: 0.6417 (mmm-85) REVERT: O 285 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.6062 (mttp) REVERT: P 265 THR cc_start: 0.4218 (OUTLIER) cc_final: 0.3941 (m) REVERT: P 269 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7461 (pttp) REVERT: P 380 VAL cc_start: 0.8279 (t) cc_final: 0.8005 (p) REVERT: P 404 GLN cc_start: 0.7570 (mt0) cc_final: 0.7360 (mt0) REVERT: Q 110 GLU cc_start: 0.6313 (tp30) cc_final: 0.6020 (tp30) REVERT: Q 181 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5353 (mt0) REVERT: Q 201 LYS cc_start: 0.7692 (tptm) cc_final: 0.7352 (ttpt) REVERT: Q 220 TYR cc_start: 0.1160 (OUTLIER) cc_final: 0.0464 (t80) REVERT: Q 346 SER cc_start: 0.8989 (m) cc_final: 0.8396 (t) REVERT: R 62 MET cc_start: 0.8095 (ttp) cc_final: 0.7866 (ttp) REVERT: R 88 MET cc_start: 0.7748 (mmm) cc_final: 0.7390 (mmm) REVERT: R 193 ILE cc_start: 0.7278 (tp) cc_final: 0.6064 (tp) REVERT: R 232 LEU cc_start: 0.6070 (tp) cc_final: 0.5719 (tt) REVERT: R 253 ARG cc_start: 0.6733 (tpp80) cc_final: 0.6449 (ttp-110) REVERT: R 446 TYR cc_start: 0.6076 (m-80) cc_final: 0.5574 (m-10) REVERT: S 121 GLN cc_start: 0.3026 (tt0) cc_final: 0.2734 (mt0) REVERT: S 123 MET cc_start: 0.2469 (mmt) cc_final: 0.2099 (ttt) REVERT: S 132 MET cc_start: 0.0824 (ptm) cc_final: 0.0378 (ptm) REVERT: S 153 MET cc_start: 0.0617 (tmm) cc_final: -0.0229 (mpp) REVERT: S 271 SER cc_start: 0.3336 (m) cc_final: 0.2999 (p) REVERT: T 82 MET cc_start: 0.0478 (mmt) cc_final: 0.0076 (mmm) REVERT: T 410 TRP cc_start: 0.0207 (m100) cc_final: -0.0212 (m100) REVERT: U 318 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5569 (m) REVERT: V 229 GLN cc_start: 0.2991 (OUTLIER) cc_final: 0.2597 (tm-30) REVERT: V 253 LYS cc_start: 0.3563 (OUTLIER) cc_final: 0.1706 (tptt) outliers start: 267 outliers final: 36 residues processed: 1263 average time/residue: 0.5836 time to fit residues: 1186.0021 Evaluate side-chains 550 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 500 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1885 TYR Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 370 ASP Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 393 HIS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 404 ARG Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 253 LYS Chi-restraints excluded: chain W residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 542 optimal weight: 30.0000 chunk 487 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 260 optimal weight: 0.7980 chunk 503 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 583 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 44 GLN D 75 HIS E 104 GLN F 44 GLN F 46 HIS F 81 ASN F 92 GLN I 99 GLN I 172 HIS I 178 GLN I 204 GLN I 903 HIS I 936 HIS I 967 HIS I1896 GLN I2060 HIS I2099 GLN J 183 ASN J 202 HIS J 330 HIS K 8 ASN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 HIS K 204 GLN K 312 HIS L 85 GLN ** M 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 HIS M 280 ASN M 305 HIS M 414 ASN N 240 HIS N 275 GLN N 302 HIS N 441 GLN N 447 GLN O 156 HIS ** O 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 241 HIS ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN O 393 HIS P 44 GLN ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 HIS Q 18 HIS ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 ASN Q 229 HIS Q 236 GLN Q 316 HIS Q 429 HIS R 25 HIS R 255 GLN R 447 GLN T 143 HIS T 252 ASN T 277 GLN T 354 ASN T 383 ASN T 407 GLN ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 296 ASN U 353 GLN ** V 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 249 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4782 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 57050 Z= 0.437 Angle : 0.790 11.896 78243 Z= 0.406 Chirality : 0.049 0.434 8827 Planarity : 0.007 0.143 9069 Dihedral : 20.470 179.526 10095 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.39 % Favored : 94.48 % Rotamer: Outliers : 3.83 % Allowed : 11.87 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.05 % 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: -1.17 (0.10), residues: 6201 helix: 0.06 (0.09), residues: 2884 sheet: -1.25 (0.17), residues: 785 loop : -1.50 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 237 HIS 0.022 0.002 HIS K 156 PHE 0.030 0.003 PHE K 88 TYR 0.026 0.002 TYR M 314 ARG 0.012 0.001 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 509 time to evaluate : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.4571 (ptpt) cc_final: 0.3744 (mmtp) REVERT: I 136 HIS cc_start: 0.0527 (OUTLIER) cc_final: -0.0099 (t-170) REVERT: I 679 MET cc_start: 0.3609 (tpp) cc_final: 0.3404 (mmm) REVERT: I 789 MET cc_start: 0.2482 (ttp) cc_final: 0.1432 (ppp) REVERT: I 1972 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8549 (pp) REVERT: I 2185 MET cc_start: 0.4557 (mmm) cc_final: 0.3966 (tpp) REVERT: I 2189 MET cc_start: 0.4362 (mmm) cc_final: 0.3510 (ptm) REVERT: J 190 TYR cc_start: 0.3407 (t80) cc_final: 0.3151 (t80) REVERT: J 310 TYR cc_start: 0.7400 (p90) cc_final: 0.7196 (p90) REVERT: K 8 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7145 (t0) REVERT: K 269 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.3877 (mmm-85) REVERT: K 336 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: L 37 ASN cc_start: 0.6375 (t0) cc_final: 0.5933 (p0) REVERT: M 165 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7685 (mptt) REVERT: M 227 ASP cc_start: 0.7583 (t0) cc_final: 0.7301 (m-30) REVERT: M 323 ILE cc_start: 0.8684 (pp) cc_final: 0.8443 (mt) REVERT: M 392 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8004 (m-40) REVERT: M 438 TYR cc_start: 0.7506 (m-80) cc_final: 0.7183 (m-80) REVERT: N 192 VAL cc_start: 0.6353 (OUTLIER) cc_final: 0.6142 (p) REVERT: N 276 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7428 (mp) REVERT: O 127 THR cc_start: 0.8078 (p) cc_final: 0.6768 (p) REVERT: O 285 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6821 (mttp) REVERT: O 364 MET cc_start: 0.7638 (mmm) cc_final: 0.7252 (mmm) REVERT: P 90 MET cc_start: 0.8611 (mtp) cc_final: 0.8382 (mtp) REVERT: P 178 MET cc_start: 0.9014 (tpp) cc_final: 0.7884 (tpp) REVERT: P 269 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7487 (mmtt) REVERT: Q 61 MET cc_start: 0.8148 (mmm) cc_final: 0.7643 (tpt) REVERT: Q 134 GLU cc_start: 0.6586 (tt0) cc_final: 0.6369 (mt-10) REVERT: Q 150 TYR cc_start: 0.4274 (m-10) cc_final: 0.4019 (m-10) REVERT: Q 201 LYS cc_start: 0.8064 (tptm) cc_final: 0.7592 (ttpt) REVERT: R 88 MET cc_start: 0.7805 (mmm) cc_final: 0.7419 (mmm) REVERT: R 193 ILE cc_start: 0.8191 (tp) cc_final: 0.7932 (tp) REVERT: R 395 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8865 (mt) REVERT: S 16 MET cc_start: 0.3739 (mpp) cc_final: 0.3483 (mpp) REVERT: S 123 MET cc_start: 0.3394 (mmt) cc_final: 0.2691 (ttt) REVERT: S 132 MET cc_start: 0.1657 (ptm) cc_final: 0.0659 (ptm) REVERT: S 153 MET cc_start: 0.0511 (tmm) cc_final: -0.0305 (mpp) REVERT: T 222 MET cc_start: 0.0832 (OUTLIER) cc_final: -0.0990 (ppp) REVERT: T 322 MET cc_start: 0.1018 (mpp) cc_final: -0.1073 (ttm) REVERT: T 410 TRP cc_start: 0.0571 (m100) cc_final: 0.0069 (m100) REVERT: U 86 TRP cc_start: 0.3056 (m-10) cc_final: 0.2469 (m-10) REVERT: V 154 LYS cc_start: 0.4428 (mtpp) cc_final: 0.3852 (ttpp) REVERT: V 253 LYS cc_start: 0.3136 (OUTLIER) cc_final: 0.1447 (mmmt) REVERT: W 196 GLU cc_start: 0.1392 (OUTLIER) cc_final: 0.0663 (tm-30) outliers start: 206 outliers final: 101 residues processed: 680 average time/residue: 0.5359 time to fit residues: 613.0125 Evaluate side-chains 504 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 389 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 858 ARG Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1885 TYR Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2050 VAL Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 TYR Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 105 CYS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 348 ILE Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 358 VAL Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 404 ARG Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 320 MET Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 222 MET Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain T residue 362 ASP Chi-restraints excluded: chain T residue 376 MET Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 253 LYS Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 324 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 485 optimal weight: 8.9990 chunk 397 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 584 optimal weight: 20.0000 chunk 631 optimal weight: 20.0000 chunk 520 optimal weight: 30.0000 chunk 580 optimal weight: 0.0980 chunk 199 optimal weight: 1.9990 chunk 469 optimal weight: 0.5980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I2039 GLN K 44 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 HIS K 272 ASN K 283 ASN M 332 ASN N 41 GLN O 169 GLN O 251 GLN ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 429 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 275 GLN ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 447 GLN ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 296 ASN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4768 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 57050 Z= 0.222 Angle : 0.606 17.669 78243 Z= 0.311 Chirality : 0.041 0.247 8827 Planarity : 0.005 0.097 9069 Dihedral : 20.263 176.646 10054 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 3.29 % Allowed : 13.19 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 6201 helix: 0.59 (0.10), residues: 2889 sheet: -0.84 (0.17), residues: 772 loop : -1.19 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 97 HIS 0.009 0.001 HIS M 316 PHE 0.024 0.001 PHE N 261 TYR 0.027 0.001 TYR K 17 ARG 0.009 0.000 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 415 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.4563 (ptpt) cc_final: 0.3743 (mmtp) REVERT: I 136 HIS cc_start: 0.0448 (OUTLIER) cc_final: -0.0132 (t-170) REVERT: I 789 MET cc_start: 0.3186 (ttp) cc_final: 0.1979 (ppp) REVERT: I 1914 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8176 (pp) REVERT: I 2086 TYR cc_start: 0.4435 (m-80) cc_final: 0.4115 (m-80) REVERT: I 2185 MET cc_start: 0.4583 (mmm) cc_final: 0.3968 (tpp) REVERT: I 2189 MET cc_start: 0.4293 (mmm) cc_final: 0.3415 (ptm) REVERT: J 152 GLN cc_start: 0.4061 (mm110) cc_final: 0.3849 (mm110) REVERT: J 190 TYR cc_start: 0.3404 (t80) cc_final: 0.3109 (t80) REVERT: K 86 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7123 (m) REVERT: K 269 ARG cc_start: 0.4848 (OUTLIER) cc_final: 0.3368 (mmm-85) REVERT: K 309 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7314 (mmm) REVERT: K 336 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: L 146 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7221 (pt0) REVERT: M 227 ASP cc_start: 0.7442 (t0) cc_final: 0.7147 (m-30) REVERT: M 364 MET cc_start: 0.8255 (mtm) cc_final: 0.7952 (mtm) REVERT: M 392 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8115 (m-40) REVERT: N 121 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: N 258 LEU cc_start: 0.5792 (mp) cc_final: 0.5526 (tp) REVERT: N 276 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7443 (mp) REVERT: O 285 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6755 (mttp) REVERT: O 364 MET cc_start: 0.7696 (mmm) cc_final: 0.7203 (mmt) REVERT: O 392 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (m-40) REVERT: O 455 MET cc_start: 0.7761 (mmm) cc_final: 0.7388 (mmm) REVERT: P 257 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.4671 (m-80) REVERT: P 269 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7381 (mmtt) REVERT: Q 61 MET cc_start: 0.8204 (mmm) cc_final: 0.7554 (tpt) REVERT: Q 150 TYR cc_start: 0.4275 (m-10) cc_final: 0.4032 (m-10) REVERT: Q 168 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.6114 (pttt) REVERT: Q 201 LYS cc_start: 0.7848 (tptm) cc_final: 0.7642 (ttpt) REVERT: Q 278 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5155 (tm-30) REVERT: Q 343 ASP cc_start: 0.8497 (t0) cc_final: 0.7964 (m-30) REVERT: R 88 MET cc_start: 0.7788 (mmm) cc_final: 0.7365 (mmm) REVERT: R 193 ILE cc_start: 0.7765 (tp) cc_final: 0.7508 (tp) REVERT: R 291 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (mp) REVERT: R 326 MET cc_start: 0.8573 (mtm) cc_final: 0.8115 (mtm) REVERT: R 423 VAL cc_start: 0.8305 (p) cc_final: 0.7988 (t) REVERT: S 16 MET cc_start: 0.3908 (mpp) cc_final: 0.3628 (mpp) REVERT: S 123 MET cc_start: 0.3281 (mmt) cc_final: 0.2486 (ttt) REVERT: S 132 MET cc_start: 0.1838 (ptm) cc_final: 0.0814 (ptm) REVERT: T 222 MET cc_start: 0.1823 (tmm) cc_final: 0.0300 (ppp) REVERT: T 322 MET cc_start: 0.0805 (mpp) cc_final: -0.1277 (ttm) REVERT: T 410 TRP cc_start: 0.0417 (m100) cc_final: 0.0002 (m100) REVERT: U 185 LEU cc_start: -0.0342 (OUTLIER) cc_final: -0.1270 (mt) REVERT: W 196 GLU cc_start: 0.1653 (OUTLIER) cc_final: 0.0922 (tm-30) outliers start: 177 outliers final: 94 residues processed: 554 average time/residue: 0.5247 time to fit residues: 496.2341 Evaluate side-chains 473 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 361 time to evaluate : 4.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 858 ARG Chi-restraints excluded: chain I residue 925 THR Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 990 VAL Chi-restraints excluded: chain I residue 1885 TYR Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1993 CYS Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 309 MET Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 390 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 105 CYS Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 392 ASN Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 404 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 320 MET Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 296 ASN Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 577 optimal weight: 2.9990 chunk 439 optimal weight: 0.8980 chunk 303 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 587 optimal weight: 20.0000 chunk 621 optimal weight: 20.0000 chunk 306 optimal weight: 3.9990 chunk 556 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 HIS K 44 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN M 332 ASN M 393 HIS M 420 ASN O 348 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 284 ASN R 233 GLN R 447 GLN S 173 HIS T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4790 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 57050 Z= 0.216 Angle : 0.592 16.184 78243 Z= 0.303 Chirality : 0.041 0.200 8827 Planarity : 0.004 0.082 9069 Dihedral : 20.133 168.683 10044 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 3.19 % Allowed : 13.99 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.05 % 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: -0.20 (0.11), residues: 6201 helix: 0.83 (0.10), residues: 2901 sheet: -0.57 (0.18), residues: 782 loop : -1.06 (0.13), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 97 HIS 0.008 0.001 HIS M 316 PHE 0.030 0.001 PHE I 963 TYR 0.018 0.001 TYR C 99 ARG 0.008 0.000 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 383 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 136 HIS cc_start: 0.1101 (OUTLIER) cc_final: 0.0349 (t-170) REVERT: I 789 MET cc_start: 0.1952 (ttp) cc_final: 0.0953 (ppp) REVERT: I 930 LEU cc_start: 0.8638 (mm) cc_final: 0.8313 (mt) REVERT: I 931 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6458 (mpp-170) REVERT: I 1972 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8462 (pp) REVERT: I 2134 VAL cc_start: 0.6078 (OUTLIER) cc_final: 0.5720 (m) REVERT: I 2185 MET cc_start: 0.4584 (mmm) cc_final: 0.3947 (tpp) REVERT: I 2189 MET cc_start: 0.4063 (mmm) cc_final: 0.3118 (ptm) REVERT: J 190 TYR cc_start: 0.3730 (t80) cc_final: 0.3337 (t80) REVERT: J 301 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5901 (p90) REVERT: K 269 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.3477 (mmm-85) REVERT: K 283 ASN cc_start: 0.6946 (OUTLIER) cc_final: 0.6689 (p0) REVERT: K 336 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: M 106 ILE cc_start: 0.8111 (tt) cc_final: 0.7862 (tt) REVERT: M 227 ASP cc_start: 0.7578 (t0) cc_final: 0.7226 (m-30) REVERT: M 364 MET cc_start: 0.8299 (mtm) cc_final: 0.8006 (mtm) REVERT: M 392 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (m-40) REVERT: M 408 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: N 113 MET cc_start: 0.8132 (mtm) cc_final: 0.7879 (ptp) REVERT: N 146 GLN cc_start: 0.7903 (mt0) cc_final: 0.7681 (mm-40) REVERT: N 147 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8242 (tp) REVERT: N 202 ILE cc_start: 0.7862 (mp) cc_final: 0.7642 (mp) REVERT: N 276 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7434 (mp) REVERT: N 390 LEU cc_start: 0.8123 (tp) cc_final: 0.7849 (tp) REVERT: O 237 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7668 (p0) REVERT: O 285 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6825 (mttp) REVERT: O 359 MET cc_start: 0.7160 (mtt) cc_final: 0.6916 (mtm) REVERT: O 403 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7903 (tp) REVERT: O 455 MET cc_start: 0.7881 (mmm) cc_final: 0.7481 (mmm) REVERT: P 167 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: P 257 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.4635 (m-80) REVERT: P 269 LYS cc_start: 0.7895 (ttpp) cc_final: 0.7366 (mmtt) REVERT: Q 61 MET cc_start: 0.8267 (mmm) cc_final: 0.7474 (tpt) REVERT: Q 150 TYR cc_start: 0.4203 (m-10) cc_final: 0.3961 (m-10) REVERT: Q 168 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6296 (pttt) REVERT: Q 201 LYS cc_start: 0.7953 (tptm) cc_final: 0.7727 (ttpt) REVERT: Q 220 TYR cc_start: 0.1172 (OUTLIER) cc_final: 0.0502 (t80) REVERT: Q 278 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5006 (tm-30) REVERT: Q 343 ASP cc_start: 0.8525 (t0) cc_final: 0.8025 (m-30) REVERT: R 88 MET cc_start: 0.7805 (mmm) cc_final: 0.7366 (mmm) REVERT: R 291 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8594 (mt) REVERT: R 292 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7792 (pt) REVERT: R 326 MET cc_start: 0.8468 (mtm) cc_final: 0.8177 (mtm) REVERT: R 423 VAL cc_start: 0.8363 (p) cc_final: 0.8115 (t) REVERT: S 123 MET cc_start: 0.3577 (mmt) cc_final: 0.2699 (ttt) REVERT: S 132 MET cc_start: 0.1189 (ptm) cc_final: 0.0267 (ptm) REVERT: T 109 MET cc_start: 0.3630 (ttm) cc_final: 0.2855 (ttm) REVERT: T 222 MET cc_start: 0.1684 (tmm) cc_final: 0.0089 (ppp) REVERT: T 322 MET cc_start: 0.0641 (mpp) cc_final: -0.1265 (ttm) REVERT: T 410 TRP cc_start: 0.0295 (m100) cc_final: -0.0083 (m100) REVERT: U 179 ASP cc_start: 0.0656 (OUTLIER) cc_final: -0.0281 (m-30) REVERT: U 185 LEU cc_start: -0.0307 (OUTLIER) cc_final: -0.1236 (mt) REVERT: W 196 GLU cc_start: 0.1671 (OUTLIER) cc_final: 0.0843 (tm-30) outliers start: 172 outliers final: 96 residues processed: 529 average time/residue: 0.5514 time to fit residues: 503.6095 Evaluate side-chains 476 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 355 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 925 THR Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 933 THR Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1885 TYR Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 1993 CYS Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 304 ASN Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 390 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 105 CYS Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 419 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 517 optimal weight: 7.9990 chunk 352 optimal weight: 6.9990 chunk 9 optimal weight: 0.0370 chunk 462 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 530 optimal weight: 8.9990 chunk 429 optimal weight: 0.4980 chunk 0 optimal weight: 40.0000 chunk 317 optimal weight: 8.9990 chunk 557 optimal weight: 0.5980 chunk 156 optimal weight: 20.0000 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN K 71 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN M 332 ASN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4780 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 57050 Z= 0.176 Angle : 0.561 16.093 78243 Z= 0.288 Chirality : 0.040 0.192 8827 Planarity : 0.004 0.081 9069 Dihedral : 20.015 172.327 10032 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.08 % Allowed : 14.25 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.03 % 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: 0.01 (0.11), residues: 6201 helix: 1.01 (0.10), residues: 2891 sheet: -0.47 (0.18), residues: 798 loop : -0.97 (0.13), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 250 HIS 0.010 0.001 HIS M 316 PHE 0.029 0.001 PHE K 102 TYR 0.017 0.001 TYR I2086 ARG 0.008 0.000 ARG I 858 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 381 time to evaluate : 5.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ILE cc_start: 0.0959 (OUTLIER) cc_final: 0.0466 (mm) REVERT: I 136 HIS cc_start: 0.1161 (OUTLIER) cc_final: 0.0485 (t-170) REVERT: I 789 MET cc_start: 0.1922 (ttp) cc_final: 0.0957 (ppp) REVERT: I 931 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6644 (mmp80) REVERT: I 1972 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8428 (pp) REVERT: I 2134 VAL cc_start: 0.5958 (OUTLIER) cc_final: 0.5679 (m) REVERT: I 2189 MET cc_start: 0.4079 (mmm) cc_final: 0.3051 (tmm) REVERT: J 190 TYR cc_start: 0.3744 (t80) cc_final: 0.3328 (t80) REVERT: J 301 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.6068 (p90) REVERT: K 86 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.7024 (m) REVERT: K 233 MET cc_start: 0.7543 (tpt) cc_final: 0.7330 (tpp) REVERT: K 269 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.3859 (mmm160) REVERT: K 283 ASN cc_start: 0.7089 (OUTLIER) cc_final: 0.6835 (p0) REVERT: K 336 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: K 354 ASN cc_start: 0.6734 (t0) cc_final: 0.6455 (t0) REVERT: M 106 ILE cc_start: 0.8020 (tt) cc_final: 0.7777 (tt) REVERT: M 227 ASP cc_start: 0.7604 (t0) cc_final: 0.7181 (m-30) REVERT: M 364 MET cc_start: 0.8308 (mtm) cc_final: 0.7914 (mtm) REVERT: M 371 MET cc_start: 0.8136 (mtp) cc_final: 0.7473 (ttm) REVERT: M 392 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: M 408 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7379 (mt0) REVERT: N 113 MET cc_start: 0.8200 (mtm) cc_final: 0.7947 (ptp) REVERT: N 121 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: N 147 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8261 (tp) REVERT: N 202 ILE cc_start: 0.7800 (mp) cc_final: 0.7527 (mp) REVERT: N 261 PHE cc_start: 0.8148 (p90) cc_final: 0.7933 (p90) REVERT: N 276 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7432 (mp) REVERT: O 237 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (p0) REVERT: O 285 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6810 (mttp) REVERT: O 403 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7802 (tp) REVERT: O 455 MET cc_start: 0.7839 (mmm) cc_final: 0.7299 (mmm) REVERT: P 167 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7841 (pp20) REVERT: P 178 MET cc_start: 0.9059 (tpt) cc_final: 0.8843 (tpt) REVERT: P 257 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.4593 (m-80) REVERT: P 269 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7129 (tppt) REVERT: Q 61 MET cc_start: 0.8274 (mmm) cc_final: 0.7498 (tpt) REVERT: Q 150 TYR cc_start: 0.4365 (m-10) cc_final: 0.4148 (m-10) REVERT: Q 168 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6336 (pttt) REVERT: Q 220 TYR cc_start: 0.1137 (OUTLIER) cc_final: 0.0540 (t80) REVERT: Q 244 ASP cc_start: 0.6761 (m-30) cc_final: 0.6427 (m-30) REVERT: Q 278 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5025 (tm-30) REVERT: Q 343 ASP cc_start: 0.8559 (t0) cc_final: 0.7892 (m-30) REVERT: R 53 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7646 (mtm180) REVERT: R 88 MET cc_start: 0.7777 (mmm) cc_final: 0.7384 (mmm) REVERT: R 90 MET cc_start: 0.8266 (mtp) cc_final: 0.8059 (mtp) REVERT: R 126 SER cc_start: 0.8886 (m) cc_final: 0.8488 (t) REVERT: R 193 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7234 (tp) REVERT: R 326 MET cc_start: 0.8446 (mtm) cc_final: 0.8022 (mtm) REVERT: R 423 VAL cc_start: 0.8392 (p) cc_final: 0.8158 (t) REVERT: S 123 MET cc_start: 0.4013 (mmt) cc_final: 0.3043 (ttt) REVERT: S 132 MET cc_start: 0.1180 (ptm) cc_final: 0.0212 (ptm) REVERT: S 325 MET cc_start: 0.3145 (tpt) cc_final: 0.2657 (tpp) REVERT: T 109 MET cc_start: 0.3277 (ttm) cc_final: 0.2883 (ttm) REVERT: T 222 MET cc_start: 0.1388 (tmm) cc_final: -0.0243 (ppp) REVERT: T 250 TRP cc_start: -0.0645 (t-100) cc_final: -0.0908 (t-100) REVERT: T 322 MET cc_start: 0.0589 (mpp) cc_final: -0.1294 (ttm) REVERT: T 410 TRP cc_start: 0.0311 (m100) cc_final: -0.0056 (m100) REVERT: U 179 ASP cc_start: 0.0670 (OUTLIER) cc_final: -0.0282 (m-30) REVERT: U 185 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.1264 (mt) REVERT: W 196 GLU cc_start: 0.1660 (OUTLIER) cc_final: 0.0833 (tm-30) outliers start: 166 outliers final: 83 residues processed: 522 average time/residue: 0.5039 time to fit residues: 453.6544 Evaluate side-chains 456 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 345 time to evaluate : 5.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 925 THR Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 933 THR Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1885 TYR Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 1993 CYS Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2090 ASP Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 307 GLU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 105 CYS Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain T residue 376 MET Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 209 optimal weight: 4.9990 chunk 559 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 364 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 622 optimal weight: 20.0000 chunk 516 optimal weight: 30.0000 chunk 288 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN I 902 ASN K 8 ASN K 85 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN O 241 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 HIS ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 348 HIS T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4865 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 57050 Z= 0.328 Angle : 0.648 17.673 78243 Z= 0.330 Chirality : 0.043 0.219 8827 Planarity : 0.005 0.093 9069 Dihedral : 20.052 173.007 10029 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 3.38 % Allowed : 14.78 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 6201 helix: 0.95 (0.10), residues: 2898 sheet: -0.53 (0.18), residues: 806 loop : -0.99 (0.13), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 97 HIS 0.012 0.001 HIS I2082 PHE 0.031 0.002 PHE I 963 TYR 0.032 0.002 TYR I2081 ARG 0.008 0.001 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 360 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ILE cc_start: 0.1077 (mm) cc_final: 0.0849 (mm) REVERT: I 136 HIS cc_start: 0.1503 (OUTLIER) cc_final: 0.0799 (t-170) REVERT: I 789 MET cc_start: 0.1951 (ttp) cc_final: 0.0987 (ppp) REVERT: I 1972 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8541 (pp) REVERT: I 2134 VAL cc_start: 0.5852 (OUTLIER) cc_final: 0.5617 (m) REVERT: I 2189 MET cc_start: 0.3550 (mmm) cc_final: 0.2357 (tmm) REVERT: J 190 TYR cc_start: 0.3758 (t80) cc_final: 0.3262 (t80) REVERT: J 324 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6664 (pttm) REVERT: K 1 MET cc_start: 0.6369 (tmm) cc_final: 0.5986 (tmm) REVERT: K 269 ARG cc_start: 0.5132 (OUTLIER) cc_final: 0.4078 (mmm160) REVERT: K 336 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: M 106 ILE cc_start: 0.8209 (tt) cc_final: 0.7942 (tt) REVERT: M 227 ASP cc_start: 0.8052 (t0) cc_final: 0.7554 (m-30) REVERT: M 364 MET cc_start: 0.8338 (mtm) cc_final: 0.7948 (mtm) REVERT: M 392 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: M 408 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: N 147 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7818 (tp) REVERT: N 185 ASP cc_start: 0.1521 (OUTLIER) cc_final: 0.0899 (p0) REVERT: N 276 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7539 (mp) REVERT: O 223 LEU cc_start: 0.8919 (tp) cc_final: 0.8686 (tp) REVERT: O 285 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6850 (mttp) REVERT: O 403 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8036 (tp) REVERT: O 432 GLU cc_start: 0.8382 (tp30) cc_final: 0.8062 (tp30) REVERT: O 455 MET cc_start: 0.8099 (mmm) cc_final: 0.7584 (mmm) REVERT: P 148 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6221 (p0) REVERT: P 167 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: P 257 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.4754 (m-80) REVERT: P 269 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7381 (tppt) REVERT: Q 61 MET cc_start: 0.8323 (mmm) cc_final: 0.8069 (tpp) REVERT: Q 168 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6974 (tttt) REVERT: Q 220 TYR cc_start: 0.1331 (OUTLIER) cc_final: 0.0977 (t80) REVERT: Q 244 ASP cc_start: 0.6865 (m-30) cc_final: 0.6606 (m-30) REVERT: Q 274 LYS cc_start: 0.7513 (tmmt) cc_final: 0.6980 (tttm) REVERT: Q 278 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5389 (tm-30) REVERT: Q 343 ASP cc_start: 0.8551 (t0) cc_final: 0.7985 (m-30) REVERT: Q 376 LYS cc_start: 0.8939 (tptt) cc_final: 0.8647 (tppp) REVERT: R 20 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: R 53 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7184 (ttp80) REVERT: R 88 MET cc_start: 0.7793 (mmm) cc_final: 0.7557 (mmt) REVERT: R 326 MET cc_start: 0.8630 (mtm) cc_final: 0.8257 (mtm) REVERT: R 423 VAL cc_start: 0.8430 (p) cc_final: 0.8158 (t) REVERT: S 123 MET cc_start: 0.3986 (mmt) cc_final: 0.2891 (ttt) REVERT: S 132 MET cc_start: 0.1716 (ptm) cc_final: 0.1021 (ptm) REVERT: T 109 MET cc_start: 0.3322 (ttm) cc_final: 0.2907 (ttm) REVERT: T 250 TRP cc_start: -0.0716 (t-100) cc_final: -0.0939 (t-100) REVERT: T 282 MET cc_start: -0.0171 (ppp) cc_final: -0.2608 (mtt) REVERT: T 322 MET cc_start: 0.0677 (mpp) cc_final: -0.1186 (ttm) REVERT: T 410 TRP cc_start: 0.0931 (m100) cc_final: 0.0643 (m100) REVERT: U 179 ASP cc_start: 0.0775 (OUTLIER) cc_final: -0.0121 (m-30) REVERT: V 119 GLU cc_start: -0.0132 (OUTLIER) cc_final: -0.1163 (tm-30) outliers start: 182 outliers final: 110 residues processed: 512 average time/residue: 0.5016 time to fit residues: 446.5792 Evaluate side-chains 459 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 326 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 925 THR Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 933 THR Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 992 MET Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 1993 CYS Chi-restraints excluded: chain I residue 2050 VAL Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 307 GLU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 390 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain O residue 451 GLN Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 430 VAL Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 376 MET Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 599 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 354 optimal weight: 1.9990 chunk 454 optimal weight: 0.7980 chunk 352 optimal weight: 3.9990 chunk 523 optimal weight: 20.0000 chunk 347 optimal weight: 0.6980 chunk 619 optimal weight: 20.0000 chunk 387 optimal weight: 2.9990 chunk 377 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN I 886 HIS I2060 HIS K 8 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4827 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 57050 Z= 0.188 Angle : 0.572 18.277 78243 Z= 0.292 Chirality : 0.040 0.262 8827 Planarity : 0.004 0.082 9069 Dihedral : 19.937 172.449 10024 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 2.82 % Allowed : 15.40 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.03 % 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: 0.12 (0.11), residues: 6201 helix: 1.09 (0.10), residues: 2908 sheet: -0.33 (0.18), residues: 798 loop : -0.95 (0.13), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 97 HIS 0.011 0.001 HIS M 316 PHE 0.026 0.001 PHE R 261 TYR 0.024 0.001 TYR J 326 ARG 0.007 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 342 time to evaluate : 4.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 GLU cc_start: 0.3995 (mp0) cc_final: 0.3056 (mm-30) REVERT: E 111 ILE cc_start: 0.1001 (mm) cc_final: 0.0779 (mm) REVERT: I 614 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5083 (mm) REVERT: I 789 MET cc_start: 0.1925 (ttp) cc_final: 0.0991 (ppp) REVERT: I 1972 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8419 (pp) REVERT: I 2134 VAL cc_start: 0.5731 (OUTLIER) cc_final: 0.5396 (m) REVERT: I 2189 MET cc_start: 0.3410 (mmm) cc_final: 0.2228 (tmm) REVERT: J 190 TYR cc_start: 0.3819 (t80) cc_final: 0.3320 (t80) REVERT: J 324 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6641 (pttm) REVERT: K 1 MET cc_start: 0.6290 (tmm) cc_final: 0.6017 (tmm) REVERT: K 172 ARG cc_start: 0.4047 (tpt170) cc_final: 0.3242 (ttp80) REVERT: K 336 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: L 101 TYR cc_start: 0.7614 (t80) cc_final: 0.6215 (t80) REVERT: M 106 ILE cc_start: 0.8100 (tt) cc_final: 0.7825 (tt) REVERT: M 225 LYS cc_start: 0.8656 (ptmt) cc_final: 0.8349 (tptt) REVERT: M 227 ASP cc_start: 0.8018 (t0) cc_final: 0.7399 (m-30) REVERT: M 364 MET cc_start: 0.8324 (mtm) cc_final: 0.8000 (mtm) REVERT: M 371 MET cc_start: 0.8205 (mtp) cc_final: 0.7825 (ttm) REVERT: M 389 GLU cc_start: 0.7961 (tp30) cc_final: 0.7469 (tp30) REVERT: M 392 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8255 (m-40) REVERT: M 408 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: N 113 MET cc_start: 0.8215 (mtm) cc_final: 0.7961 (ptp) REVERT: N 121 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: N 147 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7793 (tp) REVERT: N 261 PHE cc_start: 0.8066 (p90) cc_final: 0.7589 (p90) REVERT: O 223 LEU cc_start: 0.8943 (tp) cc_final: 0.8724 (tp) REVERT: O 285 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6696 (mttp) REVERT: O 403 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7939 (tp) REVERT: O 455 MET cc_start: 0.7763 (mmm) cc_final: 0.7306 (mmm) REVERT: P 167 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: P 257 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.4790 (m-80) REVERT: P 269 LYS cc_start: 0.7814 (ttpp) cc_final: 0.7198 (tppt) REVERT: Q 61 MET cc_start: 0.8361 (mmm) cc_final: 0.8054 (tpp) REVERT: Q 168 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6739 (ptmt) REVERT: Q 220 TYR cc_start: 0.1247 (OUTLIER) cc_final: 0.0664 (t80) REVERT: Q 244 ASP cc_start: 0.6951 (m-30) cc_final: 0.6488 (m-30) REVERT: Q 274 LYS cc_start: 0.7310 (tmmt) cc_final: 0.6754 (tttm) REVERT: Q 343 ASP cc_start: 0.8577 (t0) cc_final: 0.7980 (m-30) REVERT: Q 356 ASP cc_start: 0.8241 (t0) cc_final: 0.7911 (t0) REVERT: R 20 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: R 53 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7306 (ttp80) REVERT: R 88 MET cc_start: 0.7818 (mmm) cc_final: 0.7586 (mmt) REVERT: R 126 SER cc_start: 0.8903 (m) cc_final: 0.8516 (t) REVERT: R 326 MET cc_start: 0.8514 (mtm) cc_final: 0.8144 (mtm) REVERT: R 423 VAL cc_start: 0.8433 (p) cc_final: 0.8188 (t) REVERT: S 123 MET cc_start: 0.3965 (mmt) cc_final: 0.2841 (ttt) REVERT: S 132 MET cc_start: 0.1618 (ptm) cc_final: 0.1106 (ptm) REVERT: T 109 MET cc_start: 0.3294 (ttm) cc_final: 0.2922 (ttm) REVERT: T 250 TRP cc_start: -0.0540 (t-100) cc_final: -0.0769 (t-100) REVERT: T 282 MET cc_start: -0.0257 (ppp) cc_final: -0.2613 (mtt) REVERT: T 322 MET cc_start: 0.0429 (mpp) cc_final: -0.1278 (ttm) REVERT: T 410 TRP cc_start: 0.0550 (m100) cc_final: 0.0308 (m100) REVERT: U 179 ASP cc_start: 0.0799 (OUTLIER) cc_final: -0.0103 (m-30) REVERT: V 119 GLU cc_start: -0.0357 (OUTLIER) cc_final: -0.1314 (tm-30) REVERT: W 29 ASN cc_start: 0.2598 (OUTLIER) cc_final: 0.1765 (t0) REVERT: W 196 GLU cc_start: 0.1925 (OUTLIER) cc_final: 0.0939 (tm-30) outliers start: 152 outliers final: 96 residues processed: 469 average time/residue: 0.5217 time to fit residues: 423.3983 Evaluate side-chains 434 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 317 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 307 GLU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain O residue 451 GLN Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 419 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 383 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 370 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 422 optimal weight: 3.9990 chunk 306 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 487 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 HIS T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 57050 Z= 0.212 Angle : 0.582 17.198 78243 Z= 0.295 Chirality : 0.041 0.334 8827 Planarity : 0.004 0.081 9069 Dihedral : 19.857 170.822 10018 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 3.01 % Allowed : 15.32 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.05 % 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: 0.20 (0.11), residues: 6201 helix: 1.16 (0.10), residues: 2906 sheet: -0.26 (0.18), residues: 808 loop : -0.90 (0.13), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 97 HIS 0.009 0.001 HIS M 316 PHE 0.034 0.001 PHE J 268 TYR 0.021 0.001 TYR S 218 ARG 0.008 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 336 time to evaluate : 4.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ILE cc_start: 0.1728 (mm) cc_final: 0.1515 (mm) REVERT: I 614 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.5024 (mm) REVERT: I 789 MET cc_start: 0.1952 (ttp) cc_final: 0.1025 (ppp) REVERT: I 1972 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8448 (pp) REVERT: I 2134 VAL cc_start: 0.5702 (OUTLIER) cc_final: 0.5363 (m) REVERT: I 2189 MET cc_start: 0.3284 (mmm) cc_final: 0.2206 (tmm) REVERT: J 190 TYR cc_start: 0.3769 (t80) cc_final: 0.3254 (t80) REVERT: K 154 PHE cc_start: 0.0547 (OUTLIER) cc_final: -0.0715 (m-80) REVERT: K 172 ARG cc_start: 0.3953 (tpt170) cc_final: 0.3076 (ttp80) REVERT: K 283 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7059 (p0) REVERT: K 336 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: L 101 TYR cc_start: 0.8012 (t80) cc_final: 0.7052 (t80) REVERT: M 106 ILE cc_start: 0.8056 (tt) cc_final: 0.7795 (tt) REVERT: M 225 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8338 (tptt) REVERT: M 227 ASP cc_start: 0.7963 (t0) cc_final: 0.7400 (m-30) REVERT: M 364 MET cc_start: 0.8355 (mtm) cc_final: 0.7821 (mtm) REVERT: M 408 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: N 46 MET cc_start: 0.8618 (ttt) cc_final: 0.8224 (ttm) REVERT: N 113 MET cc_start: 0.8339 (mtm) cc_final: 0.7833 (ptp) REVERT: N 121 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: N 147 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7825 (tp) REVERT: N 185 ASP cc_start: 0.1437 (OUTLIER) cc_final: 0.1115 (p0) REVERT: N 261 PHE cc_start: 0.8282 (p90) cc_final: 0.7870 (p90) REVERT: O 403 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7953 (tp) REVERT: O 455 MET cc_start: 0.7911 (mmm) cc_final: 0.7448 (mmm) REVERT: P 167 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: P 257 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.4785 (m-80) REVERT: P 269 LYS cc_start: 0.7963 (ttpp) cc_final: 0.7233 (tppt) REVERT: Q 61 MET cc_start: 0.8384 (mmm) cc_final: 0.7526 (tpt) REVERT: Q 168 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6833 (ptmt) REVERT: Q 184 ARG cc_start: 0.7327 (ttp80) cc_final: 0.7102 (ttp80) REVERT: Q 220 TYR cc_start: 0.1431 (OUTLIER) cc_final: 0.0945 (t80) REVERT: Q 244 ASP cc_start: 0.6992 (m-30) cc_final: 0.6755 (m-30) REVERT: Q 343 ASP cc_start: 0.8543 (t0) cc_final: 0.7952 (m-30) REVERT: Q 356 ASP cc_start: 0.8312 (t0) cc_final: 0.7949 (t0) REVERT: R 20 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: R 53 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.6998 (ttp80) REVERT: R 88 MET cc_start: 0.7848 (mmm) cc_final: 0.7613 (mmt) REVERT: R 126 SER cc_start: 0.8903 (m) cc_final: 0.8506 (t) REVERT: R 326 MET cc_start: 0.8507 (mtm) cc_final: 0.8145 (mtm) REVERT: R 423 VAL cc_start: 0.8434 (p) cc_final: 0.8188 (t) REVERT: S 123 MET cc_start: 0.3962 (mmt) cc_final: 0.2817 (ttt) REVERT: S 132 MET cc_start: 0.1644 (ptm) cc_final: 0.1234 (ptm) REVERT: S 355 MET cc_start: 0.1123 (OUTLIER) cc_final: -0.0647 (tpt) REVERT: T 222 MET cc_start: 0.2102 (tmm) cc_final: 0.1451 (ppp) REVERT: T 282 MET cc_start: -0.0532 (ppp) cc_final: -0.2799 (mtt) REVERT: U 179 ASP cc_start: 0.0871 (OUTLIER) cc_final: -0.0002 (m-30) REVERT: W 29 ASN cc_start: 0.2648 (OUTLIER) cc_final: 0.1901 (t0) REVERT: W 196 GLU cc_start: 0.1935 (OUTLIER) cc_final: 0.0938 (tm-30) outliers start: 162 outliers final: 111 residues processed: 475 average time/residue: 0.5033 time to fit residues: 412.9092 Evaluate side-chains 451 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 319 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 307 GLU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 390 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain O residue 451 GLN Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 419 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 563 optimal weight: 10.0000 chunk 593 optimal weight: 20.0000 chunk 541 optimal weight: 30.0000 chunk 577 optimal weight: 0.8980 chunk 347 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 453 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 521 optimal weight: 50.0000 chunk 546 optimal weight: 8.9990 chunk 575 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 855 HIS I2084 HIS ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 GLN ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 57050 Z= 0.214 Angle : 0.586 17.288 78243 Z= 0.296 Chirality : 0.041 0.353 8827 Planarity : 0.004 0.080 9069 Dihedral : 19.820 171.512 10014 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 2.71 % Allowed : 15.77 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.03 % 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: 0.26 (0.11), residues: 6201 helix: 1.21 (0.10), residues: 2898 sheet: -0.26 (0.18), residues: 796 loop : -0.87 (0.13), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 277 HIS 0.009 0.001 HIS M 316 PHE 0.025 0.001 PHE J 274 TYR 0.021 0.001 TYR S 218 ARG 0.007 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 339 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 GLU cc_start: 0.3951 (mp0) cc_final: 0.3300 (mm-30) REVERT: I 614 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4695 (mm) REVERT: I 789 MET cc_start: 0.1758 (ttp) cc_final: 0.0844 (ppp) REVERT: I 1972 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8460 (pp) REVERT: I 2134 VAL cc_start: 0.5679 (OUTLIER) cc_final: 0.5327 (m) REVERT: I 2189 MET cc_start: 0.3327 (mmm) cc_final: 0.2167 (tmm) REVERT: J 190 TYR cc_start: 0.3890 (t80) cc_final: 0.3341 (t80) REVERT: K 154 PHE cc_start: 0.0557 (OUTLIER) cc_final: -0.0600 (m-80) REVERT: K 172 ARG cc_start: 0.4010 (tpt170) cc_final: 0.3150 (ttp80) REVERT: K 283 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7320 (p0) REVERT: K 336 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: L 101 TYR cc_start: 0.8269 (t80) cc_final: 0.7495 (t80) REVERT: M 106 ILE cc_start: 0.8090 (tt) cc_final: 0.7825 (tt) REVERT: M 225 LYS cc_start: 0.8619 (ptmt) cc_final: 0.8351 (tptt) REVERT: M 227 ASP cc_start: 0.7999 (t0) cc_final: 0.7421 (m-30) REVERT: M 364 MET cc_start: 0.8367 (mtm) cc_final: 0.7873 (mtm) REVERT: M 408 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: N 113 MET cc_start: 0.8341 (mtm) cc_final: 0.7849 (ptp) REVERT: N 121 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: N 185 ASP cc_start: 0.1529 (OUTLIER) cc_final: 0.1200 (p0) REVERT: N 261 PHE cc_start: 0.8307 (p90) cc_final: 0.7991 (p90) REVERT: O 61 MET cc_start: 0.8759 (tpp) cc_final: 0.8283 (mmm) REVERT: O 364 MET cc_start: 0.7889 (mmm) cc_final: 0.7442 (mmm) REVERT: O 403 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7904 (tp) REVERT: O 455 MET cc_start: 0.7918 (mmm) cc_final: 0.7346 (mmm) REVERT: P 167 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: P 257 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.4793 (m-80) REVERT: P 269 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7208 (tppt) REVERT: Q 61 MET cc_start: 0.8353 (mmm) cc_final: 0.7466 (tpt) REVERT: Q 168 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7007 (ptmt) REVERT: Q 220 TYR cc_start: 0.1298 (OUTLIER) cc_final: 0.0900 (t80) REVERT: Q 343 ASP cc_start: 0.8574 (t0) cc_final: 0.7970 (m-30) REVERT: Q 356 ASP cc_start: 0.8309 (t0) cc_final: 0.7941 (t0) REVERT: R 20 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: R 53 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.6925 (ttp80) REVERT: R 88 MET cc_start: 0.7827 (mmm) cc_final: 0.7604 (mmt) REVERT: R 126 SER cc_start: 0.8896 (m) cc_final: 0.8511 (t) REVERT: R 132 LYS cc_start: 0.7549 (ptpt) cc_final: 0.7158 (pptt) REVERT: R 253 ARG cc_start: 0.6748 (mtt90) cc_final: 0.6526 (mtt90) REVERT: R 274 GLU cc_start: 0.7207 (mp0) cc_final: 0.6970 (mp0) REVERT: R 326 MET cc_start: 0.8510 (mtm) cc_final: 0.8156 (mtm) REVERT: R 423 VAL cc_start: 0.8435 (p) cc_final: 0.8191 (t) REVERT: S 123 MET cc_start: 0.3935 (mmt) cc_final: 0.2804 (ttt) REVERT: S 132 MET cc_start: 0.1631 (ptm) cc_final: 0.1208 (ptm) REVERT: S 355 MET cc_start: 0.0918 (OUTLIER) cc_final: -0.0905 (tpt) REVERT: T 109 MET cc_start: 0.3405 (ttm) cc_final: 0.2933 (ttm) REVERT: T 222 MET cc_start: 0.2000 (tmm) cc_final: 0.1391 (ppp) REVERT: T 282 MET cc_start: -0.0809 (ppp) cc_final: -0.2876 (mtt) REVERT: U 179 ASP cc_start: 0.0928 (OUTLIER) cc_final: 0.0622 (m-30) REVERT: W 29 ASN cc_start: 0.2801 (OUTLIER) cc_final: 0.2017 (t0) REVERT: W 196 GLU cc_start: 0.1942 (OUTLIER) cc_final: 0.0949 (tm-30) outliers start: 146 outliers final: 108 residues processed: 462 average time/residue: 0.5063 time to fit residues: 403.8735 Evaluate side-chains 451 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 323 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 931 ARG Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 390 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 419 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 153 MET Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 379 optimal weight: 0.9990 chunk 610 optimal weight: 0.8980 chunk 372 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 chunk 640 optimal weight: 20.0000 chunk 589 optimal weight: 5.9990 chunk 510 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 886 HIS I1896 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** K 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN W 160 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 57050 Z= 0.198 Angle : 0.582 17.100 78243 Z= 0.294 Chirality : 0.040 0.345 8827 Planarity : 0.004 0.081 9069 Dihedral : 19.764 171.022 10012 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.84 % Favored : 95.11 % Rotamer: Outliers : 2.41 % Allowed : 16.10 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 6201 helix: 1.24 (0.10), residues: 2898 sheet: -0.21 (0.18), residues: 789 loop : -0.86 (0.13), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 410 HIS 0.010 0.001 HIS I 886 PHE 0.023 0.001 PHE R 261 TYR 0.021 0.001 TYR S 218 ARG 0.011 0.000 ARG Q 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 341 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.5244 (mmtt) cc_final: 0.4809 (mtpt) REVERT: D 52 GLU cc_start: 0.3954 (mp0) cc_final: 0.3289 (mm-30) REVERT: E 111 ILE cc_start: 0.1664 (mm) cc_final: 0.1389 (mm) REVERT: H 84 MET cc_start: 0.5322 (ppp) cc_final: 0.5056 (ppp) REVERT: I 614 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4748 (mm) REVERT: I 789 MET cc_start: 0.1504 (ttp) cc_final: 0.0240 (ppp) REVERT: I 1884 PHE cc_start: 0.5371 (m-10) cc_final: 0.4906 (m-80) REVERT: I 1972 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8462 (pp) REVERT: I 2134 VAL cc_start: 0.5605 (OUTLIER) cc_final: 0.5258 (m) REVERT: I 2189 MET cc_start: 0.3361 (mmm) cc_final: 0.2153 (tmm) REVERT: J 190 TYR cc_start: 0.3895 (t80) cc_final: 0.3343 (t80) REVERT: K 154 PHE cc_start: 0.0563 (OUTLIER) cc_final: -0.0587 (m-80) REVERT: K 172 ARG cc_start: 0.3941 (tpt170) cc_final: 0.3099 (ttp80) REVERT: K 336 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: M 106 ILE cc_start: 0.8052 (tt) cc_final: 0.7781 (tt) REVERT: M 225 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8344 (tptt) REVERT: M 227 ASP cc_start: 0.7995 (t0) cc_final: 0.7420 (m-30) REVERT: M 364 MET cc_start: 0.8412 (mtm) cc_final: 0.7932 (mtm) REVERT: M 408 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: N 113 MET cc_start: 0.8312 (mtm) cc_final: 0.7862 (ptp) REVERT: N 121 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: N 261 PHE cc_start: 0.8306 (p90) cc_final: 0.8009 (p90) REVERT: O 61 MET cc_start: 0.8718 (tpp) cc_final: 0.8283 (mmm) REVERT: O 403 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7784 (tp) REVERT: O 455 MET cc_start: 0.7891 (mmm) cc_final: 0.7326 (mmm) REVERT: P 167 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: P 269 LYS cc_start: 0.7949 (ttpp) cc_final: 0.7212 (tppt) REVERT: Q 61 MET cc_start: 0.8376 (mmm) cc_final: 0.7530 (tpt) REVERT: Q 150 TYR cc_start: 0.4057 (m-10) cc_final: 0.3839 (m-10) REVERT: Q 168 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7267 (ptmt) REVERT: Q 184 ARG cc_start: 0.7495 (ttp80) cc_final: 0.7227 (ttp80) REVERT: Q 220 TYR cc_start: 0.1340 (OUTLIER) cc_final: 0.1010 (t80) REVERT: Q 343 ASP cc_start: 0.8541 (t0) cc_final: 0.7939 (m-30) REVERT: Q 356 ASP cc_start: 0.8312 (t0) cc_final: 0.7939 (t0) REVERT: R 20 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: R 53 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7000 (ttp80) REVERT: R 88 MET cc_start: 0.7822 (mmm) cc_final: 0.7600 (mmt) REVERT: R 126 SER cc_start: 0.8877 (m) cc_final: 0.8515 (t) REVERT: R 132 LYS cc_start: 0.7571 (ptpt) cc_final: 0.7174 (pptt) REVERT: R 253 ARG cc_start: 0.6699 (mtt90) cc_final: 0.6492 (mtt90) REVERT: R 274 GLU cc_start: 0.7101 (mp0) cc_final: 0.6772 (mp0) REVERT: R 326 MET cc_start: 0.8495 (mtm) cc_final: 0.8137 (mtm) REVERT: R 423 VAL cc_start: 0.8446 (p) cc_final: 0.8204 (t) REVERT: S 123 MET cc_start: 0.3912 (mmt) cc_final: 0.2834 (ttt) REVERT: S 132 MET cc_start: 0.1588 (ptm) cc_final: 0.1099 (ptm) REVERT: S 355 MET cc_start: 0.0869 (OUTLIER) cc_final: -0.0789 (tpt) REVERT: T 109 MET cc_start: 0.3314 (ttm) cc_final: 0.2855 (ttm) REVERT: T 222 MET cc_start: 0.1907 (tmm) cc_final: 0.1292 (ppp) REVERT: T 282 MET cc_start: -0.0943 (ppp) cc_final: -0.2849 (mtt) REVERT: U 179 ASP cc_start: 0.0983 (OUTLIER) cc_final: 0.0733 (m-30) REVERT: W 29 ASN cc_start: 0.2959 (OUTLIER) cc_final: 0.2206 (t0) REVERT: W 196 GLU cc_start: 0.1945 (OUTLIER) cc_final: 0.0947 (tm-30) outliers start: 130 outliers final: 101 residues processed: 454 average time/residue: 0.5235 time to fit residues: 408.3487 Evaluate side-chains 447 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 329 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 390 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 127 THR Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain O residue 451 GLN Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 419 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 179 ASP Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 196 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 405 optimal weight: 0.9980 chunk 543 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 470 optimal weight: 50.0000 chunk 75 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 510 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 524 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS I 176 GLN I2175 ASN ** K 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN M 429 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 313 ASN ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 GLN T 277 GLN ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN W 160 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.160581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.106526 restraints weight = 144002.164| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.91 r_work: 0.3370 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 57050 Z= 0.434 Angle : 0.719 18.418 78243 Z= 0.366 Chirality : 0.046 0.375 8827 Planarity : 0.005 0.077 9069 Dihedral : 19.962 173.708 10012 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 2.43 % Allowed : 16.27 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 6201 helix: 0.90 (0.10), residues: 2906 sheet: -0.46 (0.18), residues: 820 loop : -1.03 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I1949 HIS 0.013 0.001 HIS I1991 PHE 0.024 0.002 PHE R 261 TYR 0.031 0.002 TYR P 446 ARG 0.013 0.001 ARG I 931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13011.59 seconds wall clock time: 228 minutes 12.13 seconds (13692.13 seconds total)