Starting phenix.real_space_refine on Thu Mar 21 03:29:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohp_12904/03_2024/7ohp_12904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohp_12904/03_2024/7ohp_12904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohp_12904/03_2024/7ohp_12904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohp_12904/03_2024/7ohp_12904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohp_12904/03_2024/7ohp_12904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohp_12904/03_2024/7ohp_12904.pdb" } resolution = 3.9 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1781 5.49 5 S 100 5.16 5 C 44096 2.51 5 N 14619 2.21 5 O 19948 1.98 5 H 63394 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 36": "OD1" <-> "OD2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "C ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 469": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H ASP 130": "OD1" <-> "OD2" Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 152": "OE1" <-> "OE2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 203": "OE1" <-> "OE2" Residue "K TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 252": "OE1" <-> "OE2" Residue "K GLU 257": "OE1" <-> "OE2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "K TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 46": "OD1" <-> "OD2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 100": "OE1" <-> "OE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 120": "OE1" <-> "OE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 27": "OD1" <-> "OD2" Residue "V ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W ASP 47": "OD1" <-> "OD2" Residue "W ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 183": "OD1" <-> "OD2" Residue "W TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 212": "OE1" <-> "OE2" Residue "W ASP 224": "OD1" <-> "OD2" Residue "W GLU 229": "OE1" <-> "OE2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 19": "OD1" <-> "OD2" Residue "b ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 301": "OE1" <-> "OE2" Residue "b ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 316": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 405": "OE1" <-> "OE2" Residue "b ASP 418": "OD1" <-> "OD2" Residue "b GLU 426": "OE1" <-> "OE2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 461": "OE1" <-> "OE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 95": "OE1" <-> "OE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i GLU 66": "OE1" <-> "OE2" Residue "i GLU 89": "OE1" <-> "OE2" Residue "j TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m GLU 342": "OE1" <-> "OE2" Residue "m GLU 350": "OE1" <-> "OE2" Residue "m ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 98": "OE1" <-> "OE2" Residue "n ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ASP 131": "OD1" <-> "OD2" Residue "n ASP 133": "OD1" <-> "OD2" Residue "n ASP 134": "OD1" <-> "OD2" Residue "n ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 196": "OE1" <-> "OE2" Residue "n GLU 207": "OE1" <-> "OE2" Residue "n ASP 214": "OD1" <-> "OD2" Residue "n TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 414": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 440": "OE1" <-> "OE2" Residue "n GLU 451": "OE1" <-> "OE2" Residue "o ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o GLU 119": "OE1" <-> "OE2" Residue "o ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ASP 198": "OD1" <-> "OD2" Residue "o ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r GLU 22": "OE1" <-> "OE2" Residue "r ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r GLU 37": "OE1" <-> "OE2" Residue "t ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ASP 83": "OD1" <-> "OD2" Residue "t GLU 89": "OE1" <-> "OE2" Residue "t PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t GLU 226": "OE1" <-> "OE2" Residue "t PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 275": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v GLU 163": "OE1" <-> "OE2" Residue "v GLU 182": "OE1" <-> "OE2" Residue "v GLU 186": "OE1" <-> "OE2" Residue "v ASP 202": "OD1" <-> "OD2" Residue "v GLU 212": "OE1" <-> "OE2" Residue "y GLU 41": "OE1" <-> "OE2" Residue "y ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 90": "OD1" <-> "OD2" Residue "y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 122": "OD1" <-> "OD2" Residue "y GLU 124": "OE1" <-> "OE2" Residue "y GLU 136": "OE1" <-> "OE2" Residue "y ASP 209": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143939 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 50411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1567, 50411 Classifications: {'RNA': 1567} Modifications used: {'3*END': 1, 'rna2p_pur': 166, 'rna2p_pyr': 114, 'rna3p_pur': 712, 'rna3p_pyr': 575} Link IDs: {'rna2p': 279, 'rna3p': 1287} Chain breaks: 44 Chain: "2" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 4764 Classifications: {'RNA': 149} Modifications used: {'3*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 60, 'rna3p_pyr': 61} Link IDs: {'rna2p': 28, 'rna3p': 120} Chain breaks: 2 Chain: "6" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 2061 Classifications: {'RNA': 65} Modifications used: {'3*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 17, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 25, 'rna3p': 39} Chain breaks: 1 Chain: "B" Number of atoms: 5374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5374 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 5071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5071 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 3 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2769 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 6 Chain: "E" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2328 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3647 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2459 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain breaks: 2 Chain: "H" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2955 Classifications: {'peptide': 181} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 176} Chain breaks: 1 Chain: "K" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3954 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 3 Chain: "L" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1782 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2064 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2733 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain breaks: 2 Chain: "O" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3171 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 1 Chain: "P" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1524 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 2 Chain: "Q" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2000 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "S" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2805 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain breaks: 1 Chain: "V" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1923 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "W" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3547 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "Y" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2060 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "b" Number of atoms: 6407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6407 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain breaks: 6 Chain: "e" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1990 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "f" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1731 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1911 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "i" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1236 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "j" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1137 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'TRANS': 69} Chain: "m" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2415 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 17, 'TRANS': 124} Chain breaks: 2 Chain: "n" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 5222 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 296} Chain breaks: 6 Chain: "o" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2009 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain breaks: 1 Chain: "r" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1288 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "t" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3684 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 216} Chain breaks: 2 Chain: "v" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2108 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 3 Chain: "y" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3398 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0HJS SG CYS j 19 128.809 94.329 134.989 1.00109.48 S ATOM A0HL5 SG CYS j 22 125.797 94.543 132.654 1.00 87.45 S ATOM A0HQU SG CYS j 34 126.838 97.591 134.666 1.00 98.44 S ATOM A0HRR SG CYS j 37 125.327 94.554 136.421 1.00 75.92 S Residues with excluded nonbonded symmetry interactions: 196 residue: pdb=" N VAL D 316 " occ=0.99 ... (14 atoms not shown) pdb="HG23 VAL D 316 " occ=0.99 residue: pdb=" N ARG D 351 " occ=0.99 ... (22 atoms not shown) pdb="HH22 ARG D 351 " occ=0.98 residue: pdb=" N VAL O 3 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (13 atoms not shown) pdb=" HG3 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (12 atoms not shown) pdb=" HD3 PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (17 atoms not shown) pdb="HD13 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (10 atoms not shown) pdb=" HB3 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (20 atoms not shown) pdb=" HZ3 LYS O 12 " occ=0.50 ... (remaining 184 not shown) Time building chain proxies: 44.54, per 1000 atoms: 0.31 Number of scatterers: 143939 At special positions: 0 Unit cell: (207.383, 269.066, 279.701, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 100 16.00 P 1781 15.00 O 19948 8.00 N 14619 7.00 C 44096 6.00 H 63394 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 97.57 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " Number of angles added : 6 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10024 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 51 sheets defined 46.2% alpha, 13.4% beta 504 base pairs and 801 stacking pairs defined. Time for finding SS restraints: 50.55 Creating SS restraints... Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 142 through 155 removed outlier: 4.551A pdb=" N LEU B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.505A pdb=" N VAL C 35 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 47 Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 141 through 145 removed outlier: 4.316A pdb=" N LYS C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.708A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 removed outlier: 4.896A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.960A pdb=" N GLY C 192 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 194 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.077A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 299 removed outlier: 4.403A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.558A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.380A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.631A pdb=" N VAL D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 303 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.975A pdb=" N ASN D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.802A pdb=" N ARG D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 347 through 351' Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.955A pdb=" N LYS D 434 " --> pdb=" O GLU D 430 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 457 Processing helix chain 'D' and resid 467 through 475 removed outlier: 3.969A pdb=" N ALA D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.041A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 152 removed outlier: 3.823A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 24 through 72 removed outlier: 3.718A pdb=" N ARG F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.846A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.682A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.820A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 174 removed outlier: 4.523A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 189 removed outlier: 4.011A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 222 removed outlier: 4.219A pdb=" N LYS G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 4.532A pdb=" N LYS G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 42 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.529A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.687A pdb=" N GLY H 119 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.811A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.777A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 78 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'K' and resid 128 through 133 Processing helix chain 'K' and resid 139 through 143 removed outlier: 4.176A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 139 through 143' Processing helix chain 'K' and resid 157 through 161 Processing helix chain 'K' and resid 166 through 176 Processing helix chain 'K' and resid 184 through 188 removed outlier: 4.328A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 200 removed outlier: 3.519A pdb=" N GLY K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLY K 196 " --> pdb=" O LYS K 192 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LYS K 197 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA K 198 " --> pdb=" O MET K 194 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.711A pdb=" N THR K 205 " --> pdb=" O VAL K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 231 Processing helix chain 'K' and resid 255 through 274 removed outlier: 3.560A pdb=" N LEU K 265 " --> pdb=" O ASP K 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE K 266 " --> pdb=" O ASN K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 298 Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.711A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.873A pdb=" N GLU N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 4.140A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU N 29 " --> pdb=" O VAL N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.759A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG O 59 " --> pdb=" O HIS O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 186 removed outlier: 3.785A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER O 164 " --> pdb=" O ARG O 160 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU O 166 " --> pdb=" O VAL O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.668A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR P 32 " --> pdb=" O ASN P 28 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN P 37 " --> pdb=" O ALA P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.527A pdb=" N GLN P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 102 removed outlier: 3.538A pdb=" N LYS P 89 " --> pdb=" O ALA P 85 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN P 92 " --> pdb=" O VAL P 88 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU P 94 " --> pdb=" O PHE P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 106 Processing helix chain 'Q' and resid 23 through 41 removed outlier: 3.558A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.238A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.542A pdb=" N GLN S 46 " --> pdb=" O TRP S 42 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.706A pdb=" N GLY S 56 " --> pdb=" O LYS S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 113 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'V' and resid 66 through 70 Processing helix chain 'V' and resid 119 through 126 removed outlier: 3.920A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.814A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.687A pdb=" N ARG W 57 " --> pdb=" O LEU W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.654A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 3.688A pdb=" N GLU W 114 " --> pdb=" O ASN W 110 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR W 115 " --> pdb=" O THR W 111 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE W 116 " --> pdb=" O VAL W 112 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 198 through 207 removed outlier: 3.650A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 60 through 64 removed outlier: 4.187A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS Y 64 " --> pdb=" O GLY Y 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 60 through 64' Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'b' and resid 14 through 26 removed outlier: 3.706A pdb=" N VAL b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG b 24 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 68 removed outlier: 4.138A pdb=" N GLU b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 114 removed outlier: 3.699A pdb=" N LYS b 92 " --> pdb=" O LYS b 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 128 Processing helix chain 'b' and resid 129 through 142 removed outlier: 3.882A pdb=" N LEU b 133 " --> pdb=" O LYS b 129 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR b 138 " --> pdb=" O GLY b 134 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS b 142 " --> pdb=" O THR b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 158 removed outlier: 3.688A pdb=" N HIS b 156 " --> pdb=" O GLN b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 removed outlier: 3.728A pdb=" N PHE b 183 " --> pdb=" O GLY b 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU b 184 " --> pdb=" O LYS b 180 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG b 185 " --> pdb=" O SER b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 Processing helix chain 'b' and resid 258 through 262 removed outlier: 4.046A pdb=" N PHE b 262 " --> pdb=" O GLN b 259 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 274 Processing helix chain 'b' and resid 274 through 279 removed outlier: 3.522A pdb=" N PHE b 278 " --> pdb=" O ILE b 274 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 274 through 279' Processing helix chain 'b' and resid 280 through 282 No H-bonds generated for 'chain 'b' and resid 280 through 282' Processing helix chain 'b' and resid 304 through 312 removed outlier: 3.586A pdb=" N SER b 308 " --> pdb=" O LEU b 305 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL b 312 " --> pdb=" O VAL b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 325 through 341 removed outlier: 3.938A pdb=" N ALA b 341 " --> pdb=" O GLU b 337 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.553A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 406 Processing helix chain 'b' and resid 440 through 444 Processing helix chain 'b' and resid 449 through 457 removed outlier: 3.545A pdb=" N ALA b 455 " --> pdb=" O ALA b 451 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU b 457 " --> pdb=" O LEU b 453 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 466 removed outlier: 3.894A pdb=" N LYS b 462 " --> pdb=" O GLU b 459 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU b 463 " --> pdb=" O GLU b 460 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU b 464 " --> pdb=" O GLU b 461 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 Processing helix chain 'e' and resid 78 through 85 removed outlier: 3.777A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.103A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'f' and resid 90 through 94 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 32 Processing helix chain 'h' and resid 43 through 70 removed outlier: 3.566A pdb=" N ALA h 65 " --> pdb=" O GLN h 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR h 70 " --> pdb=" O VAL h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 85 through 90 Processing helix chain 'h' and resid 93 through 98 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 35 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 77 removed outlier: 3.581A pdb=" N LYS i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 100 removed outlier: 3.646A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 68 through 76 removed outlier: 4.365A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 267 Processing helix chain 'm' and resid 269 through 285 removed outlier: 3.876A pdb=" N ARG m 275 " --> pdb=" O ASN m 271 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 297 Processing helix chain 'm' and resid 341 through 345 Processing helix chain 'm' and resid 347 through 357 Processing helix chain 'm' and resid 373 through 377 Processing helix chain 'm' and resid 382 through 397 removed outlier: 3.806A pdb=" N ASP m 393 " --> pdb=" O GLU m 389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR m 395 " --> pdb=" O SER m 391 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 removed outlier: 3.580A pdb=" N ARG n 34 " --> pdb=" O ALA n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 64 through 73 removed outlier: 3.666A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 Processing helix chain 'n' and resid 98 through 106 removed outlier: 4.022A pdb=" N ALA n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU n 106 " --> pdb=" O ALA n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 143 removed outlier: 3.827A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 removed outlier: 3.501A pdb=" N ILE n 156 " --> pdb=" O SER n 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA n 168 " --> pdb=" O ASN n 164 " (cutoff:3.500A) Processing helix chain 'n' and resid 214 through 241 removed outlier: 3.804A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE n 231 " --> pdb=" O THR n 227 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 384 removed outlier: 3.896A pdb=" N PHE n 378 " --> pdb=" O ASP n 374 " (cutoff:3.500A) Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.576A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS n 438 " --> pdb=" O ASP n 434 " (cutoff:3.500A) Processing helix chain 'n' and resid 443 through 447 removed outlier: 3.668A pdb=" N LYS n 446 " --> pdb=" O PRO n 443 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 113 through 115 No H-bonds generated for 'chain 'o' and resid 113 through 115' Processing helix chain 'o' and resid 141 through 152 Processing helix chain 'o' and resid 196 through 211 Processing helix chain 'o' and resid 212 through 214 No H-bonds generated for 'chain 'o' and resid 212 through 214' Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 40 removed outlier: 3.721A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA r 39 " --> pdb=" O ILE r 35 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN r 40 " --> pdb=" O SER r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 Processing helix chain 't' and resid 57 through 88 removed outlier: 4.064A pdb=" N ILE t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 167 Processing helix chain 't' and resid 183 through 190 removed outlier: 3.802A pdb=" N LEU t 187 " --> pdb=" O VAL t 183 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 232 through 238 Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 269 removed outlier: 3.771A pdb=" N GLN t 269 " --> pdb=" O ASN t 265 " (cutoff:3.500A) Processing helix chain 't' and resid 281 through 299 removed outlier: 4.125A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU t 293 " --> pdb=" O ILE t 289 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA t 294 " --> pdb=" O LYS t 290 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU t 295 " --> pdb=" O GLN t 291 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER t 296 " --> pdb=" O ARG t 292 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG t 297 " --> pdb=" O GLU t 293 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 317 removed outlier: 3.673A pdb=" N SER t 316 " --> pdb=" O ASP t 313 " (cutoff:3.500A) Processing helix chain 'v' and resid 6 through 11 Processing helix chain 'v' and resid 22 through 26 removed outlier: 3.548A pdb=" N ARG v 26 " --> pdb=" O ASP v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 40 removed outlier: 3.680A pdb=" N ASN v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 156 through 163 removed outlier: 3.680A pdb=" N LYS v 161 " --> pdb=" O GLU v 157 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU v 163 " --> pdb=" O VAL v 159 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 193 Processing helix chain 'v' and resid 195 through 201 removed outlier: 3.631A pdb=" N PHE v 201 " --> pdb=" O LYS v 197 " (cutoff:3.500A) Processing helix chain 'v' and resid 211 through 225 removed outlier: 3.607A pdb=" N LYS v 216 " --> pdb=" O GLU v 212 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG v 221 " --> pdb=" O ARG v 217 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG v 225 " --> pdb=" O ARG v 221 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 10 Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.812A pdb=" N ALA y 37 " --> pdb=" O ASN y 33 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU y 39 " --> pdb=" O TYR y 35 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 86 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 122 through 134 removed outlier: 4.250A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP y 131 " --> pdb=" O GLU y 127 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL y 132 " --> pdb=" O LEU y 128 " (cutoff:3.500A) Processing helix chain 'y' and resid 141 through 145 Processing helix chain 'y' and resid 147 through 152 removed outlier: 4.373A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.840A pdb=" N SER y 175 " --> pdb=" O GLU y 171 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 59 removed outlier: 4.679A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 78 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 324 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 279 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.435A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.435A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 15 through 21 removed outlier: 4.545A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 209 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'D' and resid 268 through 269 Processing sheet with id=AA8, first strand: chain 'D' and resid 345 through 346 removed outlier: 7.610A pdb=" N CYS D 345 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 294 " --> pdb=" O CYS D 345 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 293 " --> pdb=" O ILE D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 77 through 79 removed outlier: 5.965A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 205 through 206 removed outlier: 3.554A pdb=" N GLY F 114 " --> pdb=" O PHE F 205 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL F 86 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.292A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 5 through 11 removed outlier: 3.509A pdb=" N ILE H 10 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE H 53 " --> pdb=" O ILE H 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 24 through 29 removed outlier: 3.614A pdb=" N LYS H 36 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 132 through 136 removed outlier: 3.553A pdb=" N TYR H 86 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 112 through 114 Processing sheet with id=AB8, first strand: chain 'K' and resid 243 through 249 removed outlier: 5.472A pdb=" N ASN K 245 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL K 83 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N HIS K 247 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE K 81 " --> pdb=" O HIS K 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU K 80 " --> pdb=" O LYS K 282 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS K 282 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL K 82 " --> pdb=" O PHE K 280 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 removed outlier: 7.061A pdb=" N LYS K 122 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU K 181 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU K 124 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASP K 183 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE K 126 " --> pdb=" O ASP K 183 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE K 207 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE K 180 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE K 209 " --> pdb=" O ILE K 180 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA K 182 " --> pdb=" O ILE K 209 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.656A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AC4, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC5, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.525A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.177A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL N 64 " --> pdb=" O PHE N 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE N 130 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 6 through 10 removed outlier: 3.742A pdb=" N LYS O 103 " --> pdb=" O ILE O 33 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.558A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS P 116 " --> pdb=" O VAL P 149 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 62 through 63 removed outlier: 3.942A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLY Q 85 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE Q 106 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL Q 87 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA Q 103 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AD3, first strand: chain 'S' and resid 25 through 31 removed outlier: 4.242A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 86 through 96 removed outlier: 3.640A pdb=" N GLY S 86 " --> pdb=" O SER S 83 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 22 through 24 removed outlier: 3.632A pdb=" N ILE V 37 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL V 58 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET V 74 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 63 through 67 removed outlier: 4.437A pdb=" N GLY W 101 " --> pdb=" O LEU W 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 121 through 123 removed outlier: 3.539A pdb=" N SER W 211 " --> pdb=" O ASP W 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AD9, first strand: chain 'Y' and resid 79 through 82 removed outlier: 6.724A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AE2, first strand: chain 'b' and resid 205 through 211 removed outlier: 5.693A pdb=" N LEU b 170 " --> pdb=" O ILE b 219 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL b 250 " --> pdb=" O MET b 284 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL b 286 " --> pdb=" O VAL b 250 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN b 288 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N MET b 254 " --> pdb=" O ASN b 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET b 318 " --> pdb=" O VAL b 285 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.068A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'f' and resid 8 through 18 removed outlier: 6.917A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR f 16 " --> pdb=" O VAL f 27 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL f 27 " --> pdb=" O TYR f 16 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ARG f 18 " --> pdb=" O PRO f 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE f 49 " --> pdb=" O GLY f 69 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AE6, first strand: chain 'n' and resid 176 through 182 removed outlier: 3.505A pdb=" N LYS n 178 " --> pdb=" O GLN n 189 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN n 189 " --> pdb=" O LYS n 178 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'n' and resid 386 through 389 removed outlier: 3.605A pdb=" N VAL n 367 " --> pdb=" O ILE n 388 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL n 364 " --> pdb=" O HIS n 409 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE n 411 " --> pdb=" O VAL n 364 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR n 366 " --> pdb=" O ILE n 411 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'o' and resid 117 through 124 removed outlier: 3.597A pdb=" N ALA o 123 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU o 167 " --> pdb=" O ILE o 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 't' and resid 174 through 178 removed outlier: 3.566A pdb=" N ILE t 144 " --> pdb=" O VAL t 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU t 142 " --> pdb=" O VAL t 177 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 't' and resid 214 through 215 removed outlier: 3.930A pdb=" N ILE t 227 " --> pdb=" O ILE t 214 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'y' and resid 2 through 5 Processing sheet with id=AF3, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.967A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'y' and resid 64 through 66 removed outlier: 3.954A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU y 71 " --> pdb=" O ALA y 64 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'y' and resid 108 through 109 removed outlier: 3.795A pdb=" N VAL y 117 " --> pdb=" O PHE y 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'y' and resid 160 through 161 1717 hydrogen bonds defined for protein. 4800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1260 hydrogen bonds 2064 hydrogen bond angles 0 basepair planarities 504 basepair parallelities 801 stacking parallelities Total time for adding SS restraints: 75.53 Time building geometry restraints manager: 102.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.26: 71888 1.26 - 1.68: 77124 1.68 - 2.11: 163 2.11 - 2.53: 0 2.53 - 2.96: 1 Bond restraints: 149176 Sorted by residual: bond pdb=" O3' A 1 936 " pdb=" P C 1 938 " ideal model delta sigma weight residual 1.607 2.959 -1.352 1.50e-02 4.44e+03 8.13e+03 bond pdb=" N GLY D 267 " pdb=" CA GLY D 267 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.39e+00 bond pdb=" N GLY B 12 " pdb=" CA GLY B 12 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.39e+00 bond pdb=" N GLY N 2 " pdb=" CA GLY N 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.22e+00 bond pdb=" N SER t 282 " pdb=" CA SER t 282 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.82e+00 ... (remaining 149171 not shown) Histogram of bond angle deviations from ideal: 49.68 - 70.67: 2 70.67 - 91.65: 0 91.65 - 112.64: 170773 112.64 - 133.63: 98093 133.63 - 154.62: 51 Bond angle restraints: 268919 Sorted by residual: angle pdb=" O3' A 1 936 " pdb=" P C 1 938 " pdb=" O5' C 1 938 " ideal model delta sigma weight residual 104.00 154.62 -50.62 1.50e+00 4.44e-01 1.14e+03 angle pdb=" C3' A 1 936 " pdb=" O3' A 1 936 " pdb=" P C 1 938 " ideal model delta sigma weight residual 120.20 150.06 -29.86 1.50e+00 4.44e-01 3.96e+02 angle pdb=" O3' A 1 936 " pdb=" P C 1 938 " pdb=" OP2 C 1 938 " ideal model delta sigma weight residual 108.00 49.68 58.32 3.00e+00 1.11e-01 3.78e+02 angle pdb=" O3' A 1 936 " pdb=" P C 1 938 " pdb=" OP1 C 1 938 " ideal model delta sigma weight residual 108.00 70.66 37.34 3.00e+00 1.11e-01 1.55e+02 angle pdb=" C2' C 6 1 " pdb=" C1' C 6 1 " pdb=" N1 C 6 1 " ideal model delta sigma weight residual 112.00 117.75 -5.75 1.50e+00 4.44e-01 1.47e+01 ... (remaining 268914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 65560 35.79 - 71.59: 5615 71.59 - 107.38: 599 107.38 - 143.17: 29 143.17 - 178.97: 37 Dihedral angle restraints: 71840 sinusoidal: 53982 harmonic: 17858 Sorted by residual: dihedral pdb=" C4' A 1 720 " pdb=" C3' A 1 720 " pdb=" C2' A 1 720 " pdb=" C1' A 1 720 " ideal model delta sinusoidal sigma weight residual -35.00 36.01 -71.01 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A 1 352 " pdb=" C3' A 1 352 " pdb=" C2' A 1 352 " pdb=" C1' A 1 352 " ideal model delta sinusoidal sigma weight residual -35.00 35.69 -70.69 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C4' U 11276 " pdb=" C3' U 11276 " pdb=" C2' U 11276 " pdb=" C1' U 11276 " ideal model delta sinusoidal sigma weight residual -35.00 34.99 -69.99 1 8.00e+00 1.56e-02 9.87e+01 ... (remaining 71837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 14532 0.066 - 0.131: 799 0.131 - 0.197: 19 0.197 - 0.263: 54 0.263 - 0.328: 3 Chirality restraints: 15407 Sorted by residual: chirality pdb=" C3' U 11276 " pdb=" C4' U 11276 " pdb=" O3' U 11276 " pdb=" C2' U 11276 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' A 1 352 " pdb=" C4' A 1 352 " pdb=" O3' A 1 352 " pdb=" C2' A 1 352 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' A 1 720 " pdb=" C4' A 1 720 " pdb=" O3' A 1 720 " pdb=" C2' A 1 720 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 15404 not shown) Planarity restraints: 15441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 11451 " 0.004 2.00e-02 2.50e+03 3.59e-02 3.54e+01 pdb=" N1 C 11451 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C 11451 " 0.089 2.00e-02 2.50e+03 pdb=" O2 C 11451 " -0.058 2.00e-02 2.50e+03 pdb=" N3 C 11451 " -0.021 2.00e-02 2.50e+03 pdb=" C4 C 11451 " 0.041 2.00e-02 2.50e+03 pdb=" N4 C 11451 " -0.020 2.00e-02 2.50e+03 pdb=" C5 C 11451 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C 11451 " -0.007 2.00e-02 2.50e+03 pdb=" H5 C 11451 " -0.008 2.00e-02 2.50e+03 pdb=" H6 C 11451 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12353 " 0.007 2.00e-02 2.50e+03 2.03e-02 1.44e+01 pdb=" N9 G 12353 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G 12353 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 12353 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 12353 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 12353 " -0.034 2.00e-02 2.50e+03 pdb=" O6 G 12353 " 0.027 2.00e-02 2.50e+03 pdb=" N1 G 12353 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G 12353 " -0.050 2.00e-02 2.50e+03 pdb=" N2 G 12353 " 0.033 2.00e-02 2.50e+03 pdb=" N3 G 12353 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G 12353 " -0.001 2.00e-02 2.50e+03 pdb=" H8 G 12353 " -0.000 2.00e-02 2.50e+03 pdb=" H1 G 12353 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 973 " -0.039 2.00e-02 2.50e+03 1.70e-02 9.34e+00 pdb=" N9 A 1 973 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A 1 973 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 973 " -0.006 2.00e-02 2.50e+03 pdb=" C5 A 1 973 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 1 973 " -0.014 2.00e-02 2.50e+03 pdb=" N6 A 1 973 " 0.000 2.00e-02 2.50e+03 pdb=" N1 A 1 973 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 973 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 973 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A 1 973 " 0.008 2.00e-02 2.50e+03 pdb=" H8 A 1 973 " 0.003 2.00e-02 2.50e+03 pdb=" H2 A 1 973 " 0.003 2.00e-02 2.50e+03 ... (remaining 15438 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 6487 2.17 - 2.78: 243271 2.78 - 3.38: 385919 3.38 - 3.99: 511700 3.99 - 4.60: 775317 Nonbonded interactions: 1922694 Sorted by model distance: nonbonded pdb=" OD1 ASN y 200 " pdb=" H LEU y 203 " model vdw 1.560 1.850 nonbonded pdb=" OP2 U 11356 " pdb=" HZ1 LYS Q 31 " model vdw 1.573 1.850 nonbonded pdb=" O2' G 11404 " pdb=" H61 A 11406 " model vdw 1.592 1.850 nonbonded pdb="HO2' G 1 74 " pdb=" O5' G 1 75 " model vdw 1.599 1.850 nonbonded pdb=" O2' G 1 760 " pdb=" H21 G 1 770 " model vdw 1.605 1.850 ... (remaining 1922689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.310 Extract box with map and model: 18.350 Check model and map are aligned: 1.590 Set scattering table: 1.020 Process input model: 429.960 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.320 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: 0.030 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 460.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 : 0.005 1.352 85782 Z= 0.254 Angle : 0.536 58.320 124338 Z= 0.273 Chirality : 0.034 0.328 15407 Planarity : 0.002 0.045 9104 Dihedral : 22.321 178.966 44068 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 1.01 % Allowed : 14.17 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.12), residues: 5134 helix: 2.02 (0.12), residues: 2001 sheet: 0.01 (0.22), residues: 572 loop : 0.02 (0.13), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP K 253 HIS 0.003 0.000 HIS y 118 PHE 0.010 0.000 PHE B 130 TYR 0.016 0.001 TYR b 420 ARG 0.005 0.000 ARG K 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 813 time to evaluate : 6.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 ASP cc_start: 0.8009 (p0) cc_final: 0.7738 (p0) REVERT: C 50 TYR cc_start: 0.8733 (p90) cc_final: 0.8473 (p90) REVERT: D 281 PHE cc_start: 0.8416 (t80) cc_final: 0.8171 (t80) REVERT: D 360 TRP cc_start: 0.8079 (m100) cc_final: 0.7875 (m100) REVERT: F 163 LEU cc_start: 0.7774 (mt) cc_final: 0.7408 (mp) REVERT: G 79 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: M 121 MET cc_start: 0.9008 (ttp) cc_final: 0.8690 (ttp) REVERT: N 31 ARG cc_start: 0.9146 (ttm170) cc_final: 0.8875 (tpp80) REVERT: O 156 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7703 (tp) REVERT: Q 22 ASP cc_start: 0.9224 (t0) cc_final: 0.8942 (t0) REVERT: W 97 SER cc_start: 0.6842 (p) cc_final: 0.6477 (m) REVERT: Y 26 GLN cc_start: 0.9295 (mm-40) cc_final: 0.9061 (tp40) REVERT: b 11 VAL cc_start: 0.8408 (t) cc_final: 0.7865 (m) REVERT: b 57 PHE cc_start: 0.9026 (m-80) cc_final: 0.8620 (m-80) REVERT: b 237 MET cc_start: 0.7074 (mpp) cc_final: 0.6536 (mmt) REVERT: b 317 ILE cc_start: 0.7962 (pt) cc_final: 0.7716 (pt) REVERT: e 54 LYS cc_start: 0.8658 (ptpt) cc_final: 0.8388 (mmmt) REVERT: f 59 VAL cc_start: 0.8318 (m) cc_final: 0.8071 (m) REVERT: o 137 LEU cc_start: 0.8310 (pt) cc_final: 0.7885 (pt) outliers start: 46 outliers final: 19 residues processed: 853 average time/residue: 1.8800 time to fit residues: 2582.5253 Evaluate side-chains 568 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 547 time to evaluate : 6.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain O residue 73 PHE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain i residue 57 LEU Chi-restraints excluded: chain n residue 88 ARG Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain t residue 151 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 583 optimal weight: 20.0000 chunk 523 optimal weight: 4.9990 chunk 290 optimal weight: 0.0050 chunk 178 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 541 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 329 optimal weight: 30.0000 chunk 403 optimal weight: 10.0000 chunk 627 optimal weight: 30.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN C 116 ASN C 213 ASN D 441 GLN F 112 ASN F 209 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN M 27 GLN M 59 ASN O 42 ASN O 50 ASN P 97 ASN P 101 ASN P 118 GLN Q 58 ASN S 89 ASN ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 HIS f 17 GLN h 59 ASN j 76 ASN o 113 GLN ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN y 86 ASN y 95 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 85782 Z= 0.204 Angle : 0.543 32.924 124338 Z= 0.279 Chirality : 0.037 1.752 15407 Planarity : 0.004 0.053 9104 Dihedral : 23.064 178.894 33326 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 1.66 % Allowed : 18.58 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.12), residues: 5134 helix: 1.55 (0.12), residues: 2047 sheet: -0.31 (0.20), residues: 666 loop : -0.21 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 354 HIS 0.004 0.001 HIS r 20 PHE 0.018 0.001 PHE D 393 TYR 0.019 0.001 TYR t 216 ARG 0.012 0.000 ARG f 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 566 time to evaluate : 6.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8831 (p90) cc_final: 0.8493 (p90) REVERT: C 196 ASN cc_start: 0.8028 (m-40) cc_final: 0.7794 (m-40) REVERT: D 459 LEU cc_start: -0.0964 (OUTLIER) cc_final: -0.1225 (tt) REVERT: F 163 LEU cc_start: 0.8025 (mt) cc_final: 0.7585 (mp) REVERT: G 161 GLU cc_start: 0.8997 (mp0) cc_final: 0.8762 (tt0) REVERT: L 27 ASP cc_start: 0.8955 (p0) cc_final: 0.8673 (p0) REVERT: M 121 MET cc_start: 0.9082 (ttp) cc_final: 0.8798 (ttp) REVERT: N 31 ARG cc_start: 0.9137 (ttm170) cc_final: 0.8897 (tpp80) REVERT: W 97 SER cc_start: 0.6912 (p) cc_final: 0.6552 (m) REVERT: Y 26 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9108 (tp40) REVERT: b 57 PHE cc_start: 0.8969 (m-80) cc_final: 0.8727 (m-80) REVERT: h 67 ARG cc_start: 0.9509 (ttm-80) cc_final: 0.9091 (ttp80) outliers start: 76 outliers final: 43 residues processed: 629 average time/residue: 1.8832 time to fit residues: 1927.6230 Evaluate side-chains 548 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 504 time to evaluate : 6.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain O residue 73 PHE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 391 SER Chi-restraints excluded: chain n residue 88 ARG Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 348 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 522 optimal weight: 20.0000 chunk 427 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 628 optimal weight: 8.9990 chunk 679 optimal weight: 20.0000 chunk 559 optimal weight: 7.9990 chunk 623 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 504 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN C 43 ASN C 92 ASN G 155 ASN ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN P 45 GLN ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN m 271 ASN ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 149 GLN ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 85782 Z= 0.202 Angle : 0.536 28.308 124338 Z= 0.276 Chirality : 0.037 1.788 15407 Planarity : 0.004 0.093 9104 Dihedral : 23.195 179.153 33305 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.95 % Favored : 95.03 % Rotamer: Outliers : 1.99 % Allowed : 18.47 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.12), residues: 5134 helix: 1.30 (0.12), residues: 2045 sheet: -0.63 (0.20), residues: 658 loop : -0.35 (0.13), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP n 166 HIS 0.012 0.001 HIS o 160 PHE 0.017 0.001 PHE D 277 TYR 0.033 0.001 TYR K 167 ARG 0.008 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 521 time to evaluate : 6.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 MET cc_start: 0.8780 (tpp) cc_final: 0.8529 (tpp) REVERT: C 50 TYR cc_start: 0.8854 (p90) cc_final: 0.8538 (p90) REVERT: C 196 ASN cc_start: 0.7971 (m-40) cc_final: 0.7752 (m-40) REVERT: D 392 MET cc_start: 0.4276 (mpp) cc_final: 0.3911 (mpp) REVERT: D 459 LEU cc_start: -0.0750 (OUTLIER) cc_final: -0.1018 (tt) REVERT: H 1 MET cc_start: 0.4259 (tpt) cc_final: 0.3962 (tpt) REVERT: L 27 ASP cc_start: 0.8966 (p0) cc_final: 0.8700 (p0) REVERT: M 121 MET cc_start: 0.9081 (ttp) cc_final: 0.8848 (ttp) REVERT: N 6 TYR cc_start: 0.8633 (m-80) cc_final: 0.8433 (m-10) REVERT: N 31 ARG cc_start: 0.9114 (ttm170) cc_final: 0.8885 (tpp80) REVERT: S 23 LYS cc_start: 0.9267 (mttt) cc_final: 0.8795 (tptp) REVERT: W 97 SER cc_start: 0.6853 (p) cc_final: 0.6473 (m) REVERT: W 217 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8207 (p) REVERT: h 67 ARG cc_start: 0.9527 (ttm-80) cc_final: 0.9128 (ttp80) REVERT: n 103 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8550 (ttpp) REVERT: o 106 GLU cc_start: 0.7921 (mp0) cc_final: 0.7314 (mp0) outliers start: 91 outliers final: 57 residues processed: 587 average time/residue: 1.8309 time to fit residues: 1735.7300 Evaluate side-chains 540 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 481 time to evaluate : 6.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 179 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 73 PHE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain V residue 97 ASP Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 57 LEU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain m residue 276 VAL Chi-restraints excluded: chain m residue 391 SER Chi-restraints excluded: chain n residue 88 ARG Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 103 HIS Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain t residue 216 TYR Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 621 optimal weight: 30.0000 chunk 472 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 69 optimal weight: 50.0000 chunk 300 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 630 optimal weight: 9.9990 chunk 667 optimal weight: 20.0000 chunk 329 optimal weight: 30.0000 chunk 597 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS B 279 ASN C 92 ASN C 116 ASN C 196 ASN F 104 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 85 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 259 GLN ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 GLN ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 85782 Z= 0.357 Angle : 0.700 24.909 124338 Z= 0.363 Chirality : 0.042 2.109 15407 Planarity : 0.005 0.079 9104 Dihedral : 23.521 179.576 33303 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.16 % Rotamer: Outliers : 3.19 % Allowed : 19.20 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 5134 helix: 0.44 (0.11), residues: 2046 sheet: -0.88 (0.19), residues: 653 loop : -0.98 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP n 166 HIS 0.009 0.002 HIS S 114 PHE 0.035 0.002 PHE t 261 TYR 0.029 0.002 TYR Q 33 ARG 0.008 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 456 time to evaluate : 6.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8925 (p90) cc_final: 0.8720 (p90) REVERT: D 459 LEU cc_start: -0.0366 (OUTLIER) cc_final: -0.0608 (tt) REVERT: H 1 MET cc_start: 0.4011 (tpt) cc_final: 0.3760 (tpt) REVERT: M 121 MET cc_start: 0.9057 (ttp) cc_final: 0.8820 (ttp) REVERT: N 31 ARG cc_start: 0.9167 (ttm170) cc_final: 0.8929 (tpp80) REVERT: S 23 LYS cc_start: 0.9408 (mttt) cc_final: 0.8962 (tptp) REVERT: W 97 SER cc_start: 0.7054 (p) cc_final: 0.6653 (m) REVERT: b 232 MET cc_start: -0.0005 (mmt) cc_final: -0.0703 (mtt) REVERT: b 317 ILE cc_start: 0.8199 (pt) cc_final: 0.7943 (mt) REVERT: h 67 ARG cc_start: 0.9555 (ttm-80) cc_final: 0.9193 (ttp80) REVERT: m 311 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.4246 (m-90) REVERT: n 149 ASN cc_start: 0.8601 (p0) cc_final: 0.8283 (p0) REVERT: n 186 VAL cc_start: 0.4745 (OUTLIER) cc_final: 0.4405 (t) REVERT: o 106 GLU cc_start: 0.7881 (mp0) cc_final: 0.7568 (mp0) outliers start: 146 outliers final: 104 residues processed: 567 average time/residue: 1.8410 time to fit residues: 1680.4881 Evaluate side-chains 533 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 426 time to evaluate : 6.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 73 PHE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 74 LYS Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 88 GLU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain m residue 276 VAL Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain m residue 391 SER Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 88 ARG Chi-restraints excluded: chain n residue 113 THR Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 253 ASP Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 69 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 90 THR Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 15 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 32 GLU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 556 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 497 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 569 optimal weight: 20.0000 chunk 461 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 341 optimal weight: 30.0000 chunk 599 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 HIS t 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 85782 Z= 0.286 Angle : 0.618 27.999 124338 Z= 0.319 Chirality : 0.039 1.815 15407 Planarity : 0.005 0.074 9104 Dihedral : 23.664 179.306 33296 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 2.80 % Allowed : 20.42 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5134 helix: 0.43 (0.11), residues: 2043 sheet: -1.06 (0.19), residues: 661 loop : -1.07 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 32 HIS 0.013 0.001 HIS S 114 PHE 0.018 0.001 PHE E 163 TYR 0.022 0.002 TYR Q 33 ARG 0.012 0.001 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 431 time to evaluate : 6.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8889 (p90) cc_final: 0.8624 (p90) REVERT: D 360 TRP cc_start: 0.8557 (m100) cc_final: 0.8335 (m100) REVERT: D 459 LEU cc_start: -0.0480 (OUTLIER) cc_final: -0.0733 (tt) REVERT: G 79 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: H 1 MET cc_start: 0.3957 (tpt) cc_final: 0.3748 (tpt) REVERT: M 121 MET cc_start: 0.9029 (ttp) cc_final: 0.8737 (ttp) REVERT: N 31 ARG cc_start: 0.9164 (ttm170) cc_final: 0.8936 (tpp80) REVERT: W 97 SER cc_start: 0.7049 (p) cc_final: 0.6663 (m) REVERT: b 232 MET cc_start: -0.0135 (mmt) cc_final: -0.1021 (mtt) REVERT: b 317 ILE cc_start: 0.8236 (pt) cc_final: 0.7981 (mt) REVERT: h 67 ARG cc_start: 0.9578 (ttm-80) cc_final: 0.9264 (ttp80) REVERT: m 311 TRP cc_start: 0.6642 (OUTLIER) cc_final: 0.4381 (m-90) REVERT: m 391 SER cc_start: 0.7239 (OUTLIER) cc_final: 0.6882 (p) REVERT: n 149 ASN cc_start: 0.8632 (p0) cc_final: 0.8282 (p0) REVERT: n 186 VAL cc_start: 0.4826 (OUTLIER) cc_final: 0.4496 (t) REVERT: o 106 GLU cc_start: 0.7913 (mp0) cc_final: 0.7657 (mp0) outliers start: 128 outliers final: 98 residues processed: 525 average time/residue: 1.8687 time to fit residues: 1587.7931 Evaluate side-chains 516 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 413 time to evaluate : 6.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 73 PHE Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 276 VAL Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain m residue 391 SER Chi-restraints excluded: chain m residue 393 ASP Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 253 ASP Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 69 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 90 THR Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 225 HIS Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 32 GLU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 224 optimal weight: 9.9990 chunk 601 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 668 optimal weight: 10.0000 chunk 554 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN C 196 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 85782 Z= 0.223 Angle : 0.578 27.139 124338 Z= 0.298 Chirality : 0.038 1.908 15407 Planarity : 0.004 0.067 9104 Dihedral : 23.651 179.514 33292 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 2.65 % Allowed : 20.86 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 5134 helix: 0.58 (0.11), residues: 2052 sheet: -1.05 (0.19), residues: 654 loop : -1.03 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 32 HIS 0.007 0.001 HIS S 114 PHE 0.031 0.001 PHE W 206 TYR 0.017 0.002 TYR h 70 ARG 0.006 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 424 time to evaluate : 6.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8865 (p90) cc_final: 0.8585 (p90) REVERT: D 454 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.6638 (t80) REVERT: D 459 LEU cc_start: -0.0488 (OUTLIER) cc_final: -0.0750 (tt) REVERT: G 79 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: H 1 MET cc_start: 0.3984 (tpt) cc_final: 0.3769 (tpt) REVERT: M 121 MET cc_start: 0.9018 (ttp) cc_final: 0.8732 (ttp) REVERT: N 31 ARG cc_start: 0.9152 (ttm170) cc_final: 0.8925 (tpp80) REVERT: W 97 SER cc_start: 0.6909 (p) cc_final: 0.6530 (m) REVERT: b 136 MET cc_start: 0.8424 (mmm) cc_final: 0.8189 (mmm) REVERT: b 143 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8474 (mp) REVERT: b 232 MET cc_start: -0.0233 (mmt) cc_final: -0.1124 (mtt) REVERT: b 317 ILE cc_start: 0.8227 (pt) cc_final: 0.7971 (mt) REVERT: h 67 ARG cc_start: 0.9600 (ttm-80) cc_final: 0.9279 (ttp80) REVERT: i 55 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8326 (mtt90) REVERT: m 311 TRP cc_start: 0.6539 (OUTLIER) cc_final: 0.4259 (m-90) REVERT: n 149 ASN cc_start: 0.8616 (p0) cc_final: 0.8266 (p0) REVERT: n 186 VAL cc_start: 0.4876 (OUTLIER) cc_final: 0.4560 (t) REVERT: y 192 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5251 (t) outliers start: 121 outliers final: 100 residues processed: 512 average time/residue: 1.7369 time to fit residues: 1444.5662 Evaluate side-chains 518 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 410 time to evaluate : 6.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 100 HIS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain m residue 391 SER Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain r residue 20 HIS Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 32 GLU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 644 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 488 optimal weight: 20.0000 chunk 378 optimal weight: 10.0000 chunk 562 optimal weight: 0.0010 chunk 373 optimal weight: 9.9990 chunk 666 optimal weight: 20.0000 chunk 416 optimal weight: 9.9990 chunk 406 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 HIS ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 85782 Z= 0.264 Angle : 0.615 28.010 124338 Z= 0.316 Chirality : 0.039 1.815 15407 Planarity : 0.004 0.064 9104 Dihedral : 23.748 179.904 33286 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 3.13 % Allowed : 20.73 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 5134 helix: 0.42 (0.11), residues: 2047 sheet: -1.12 (0.20), residues: 640 loop : -1.25 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 32 HIS 0.010 0.001 HIS O 72 PHE 0.029 0.002 PHE t 261 TYR 0.021 0.002 TYR K 230 ARG 0.006 0.001 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 408 time to evaluate : 6.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8873 (p90) cc_final: 0.8568 (p90) REVERT: D 454 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7015 (t80) REVERT: D 459 LEU cc_start: -0.0644 (OUTLIER) cc_final: -0.0933 (tt) REVERT: G 79 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: G 202 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8275 (mm-30) REVERT: K 97 LEU cc_start: 0.7758 (tp) cc_final: 0.7551 (tp) REVERT: K 255 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8457 (mmp80) REVERT: M 121 MET cc_start: 0.9027 (ttp) cc_final: 0.8725 (ttp) REVERT: N 31 ARG cc_start: 0.9187 (ttm170) cc_final: 0.8946 (tpp80) REVERT: O 58 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7195 (tt) REVERT: V 74 MET cc_start: 0.7423 (ppp) cc_final: 0.6226 (ppp) REVERT: W 97 SER cc_start: 0.6638 (p) cc_final: 0.6242 (m) REVERT: W 217 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8168 (p) REVERT: b 136 MET cc_start: 0.8473 (mmm) cc_final: 0.8226 (mmm) REVERT: b 143 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8521 (mp) REVERT: b 232 MET cc_start: 0.0122 (mmt) cc_final: -0.0843 (mtt) REVERT: b 317 ILE cc_start: 0.8251 (pt) cc_final: 0.7992 (mt) REVERT: e 54 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9009 (mmmt) REVERT: e 66 LEU cc_start: 0.8258 (mm) cc_final: 0.7996 (mm) REVERT: h 67 ARG cc_start: 0.9611 (ttm-80) cc_final: 0.9294 (ttp80) REVERT: i 55 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8228 (mtt90) REVERT: m 311 TRP cc_start: 0.6626 (OUTLIER) cc_final: 0.4395 (m-90) REVERT: n 149 ASN cc_start: 0.8562 (p0) cc_final: 0.8196 (p0) REVERT: n 186 VAL cc_start: 0.4837 (OUTLIER) cc_final: 0.4558 (t) REVERT: t 257 MET cc_start: 0.4623 (mmm) cc_final: 0.4354 (mmp) REVERT: y 192 VAL cc_start: 0.5692 (OUTLIER) cc_final: 0.5469 (t) outliers start: 143 outliers final: 111 residues processed: 515 average time/residue: 1.7574 time to fit residues: 1472.4287 Evaluate side-chains 518 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 396 time to evaluate : 6.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 72 HIS Chi-restraints excluded: chain O residue 73 PHE Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 120 GLU Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 205 GLN Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 100 HIS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 253 ASP Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain o residue 158 MET Chi-restraints excluded: chain r residue 20 HIS Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 69 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 32 GLU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 412 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 chunk 397 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 423 optimal weight: 0.9980 chunk 453 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 85782 Z= 0.233 Angle : 0.591 27.284 124338 Z= 0.303 Chirality : 0.039 1.895 15407 Planarity : 0.004 0.066 9104 Dihedral : 23.799 179.641 33286 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.23 % Favored : 93.73 % Rotamer: Outliers : 2.73 % Allowed : 21.25 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 5134 helix: 0.54 (0.11), residues: 2045 sheet: -1.09 (0.20), residues: 637 loop : -1.22 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 32 HIS 0.006 0.001 HIS B 198 PHE 0.049 0.001 PHE i 80 TYR 0.015 0.002 TYR L 89 ARG 0.011 0.000 ARG v 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 399 time to evaluate : 6.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8860 (p90) cc_final: 0.8648 (p90) REVERT: D 454 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.6984 (t80) REVERT: D 459 LEU cc_start: -0.0626 (OUTLIER) cc_final: -0.0954 (tt) REVERT: G 79 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: G 202 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8200 (mm-30) REVERT: K 97 LEU cc_start: 0.7738 (tp) cc_final: 0.7537 (tp) REVERT: M 121 MET cc_start: 0.9028 (ttp) cc_final: 0.8697 (ttp) REVERT: N 31 ARG cc_start: 0.9189 (ttm170) cc_final: 0.8946 (tpp80) REVERT: W 97 SER cc_start: 0.6677 (p) cc_final: 0.6282 (m) REVERT: W 217 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8136 (p) REVERT: b 136 MET cc_start: 0.8431 (mmm) cc_final: 0.8179 (mmm) REVERT: b 143 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8530 (mp) REVERT: b 232 MET cc_start: 0.0274 (mmt) cc_final: -0.0683 (mtt) REVERT: b 317 ILE cc_start: 0.8248 (pt) cc_final: 0.7992 (mt) REVERT: e 54 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8994 (mmmt) REVERT: e 66 LEU cc_start: 0.8275 (mm) cc_final: 0.8034 (mm) REVERT: h 67 ARG cc_start: 0.9607 (ttm-80) cc_final: 0.9299 (ttp80) REVERT: m 311 TRP cc_start: 0.6582 (OUTLIER) cc_final: 0.4409 (m-90) REVERT: n 149 ASN cc_start: 0.8639 (p0) cc_final: 0.8280 (p0) REVERT: n 186 VAL cc_start: 0.4871 (OUTLIER) cc_final: 0.4601 (t) REVERT: y 192 VAL cc_start: 0.5538 (OUTLIER) cc_final: 0.5305 (t) outliers start: 125 outliers final: 107 residues processed: 493 average time/residue: 1.6626 time to fit residues: 1336.7624 Evaluate side-chains 504 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 388 time to evaluate : 6.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 100 HIS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 253 ASP Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain r residue 20 HIS Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 69 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 32 GLU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 605 optimal weight: 10.0000 chunk 638 optimal weight: 10.0000 chunk 582 optimal weight: 20.0000 chunk 620 optimal weight: 20.0000 chunk 637 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 487 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 560 optimal weight: 4.9990 chunk 586 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 85782 Z= 0.251 Angle : 0.606 27.639 124338 Z= 0.311 Chirality : 0.039 1.851 15407 Planarity : 0.004 0.058 9104 Dihedral : 23.854 179.351 33286 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 2.84 % Allowed : 21.14 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 5134 helix: 0.46 (0.11), residues: 2041 sheet: -1.21 (0.20), residues: 627 loop : -1.26 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 32 HIS 0.006 0.001 HIS O 72 PHE 0.023 0.001 PHE G 165 TYR 0.014 0.002 TYR W 220 ARG 0.008 0.000 ARG K 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 393 time to evaluate : 6.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8864 (p90) cc_final: 0.8572 (p90) REVERT: D 454 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7297 (t80) REVERT: D 459 LEU cc_start: -0.0428 (OUTLIER) cc_final: -0.0781 (tt) REVERT: K 97 LEU cc_start: 0.7752 (tp) cc_final: 0.7550 (tp) REVERT: M 121 MET cc_start: 0.9040 (ttp) cc_final: 0.8734 (ttp) REVERT: N 31 ARG cc_start: 0.9178 (ttm170) cc_final: 0.8938 (tpp80) REVERT: V 74 MET cc_start: 0.7618 (ppp) cc_final: 0.6422 (ppp) REVERT: W 97 SER cc_start: 0.6616 (p) cc_final: 0.6216 (m) REVERT: b 136 MET cc_start: 0.8470 (mmm) cc_final: 0.8203 (mmm) REVERT: b 143 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8561 (mp) REVERT: b 232 MET cc_start: 0.0518 (mmt) cc_final: -0.0461 (mtt) REVERT: b 317 ILE cc_start: 0.8261 (pt) cc_final: 0.8006 (mt) REVERT: e 54 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9006 (mmmt) REVERT: e 66 LEU cc_start: 0.8415 (mm) cc_final: 0.8116 (mm) REVERT: h 67 ARG cc_start: 0.9605 (ttm-80) cc_final: 0.9358 (ttp80) REVERT: i 55 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8240 (mtt90) REVERT: m 311 TRP cc_start: 0.6581 (OUTLIER) cc_final: 0.4512 (m-90) REVERT: n 149 ASN cc_start: 0.8580 (p0) cc_final: 0.8207 (p0) REVERT: n 186 VAL cc_start: 0.4786 (OUTLIER) cc_final: 0.4493 (t) REVERT: o 106 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7415 (mm-30) REVERT: y 192 VAL cc_start: 0.5692 (OUTLIER) cc_final: 0.5450 (t) outliers start: 130 outliers final: 117 residues processed: 491 average time/residue: 1.6873 time to fit residues: 1352.4997 Evaluate side-chains 511 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 386 time to evaluate : 6.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 72 HIS Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 100 HIS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 253 ASP Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain r residue 20 HIS Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 69 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 291 GLN Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 32 GLU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 618 optimal weight: 8.9990 chunk 407 optimal weight: 5.9990 chunk 656 optimal weight: 20.0000 chunk 400 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 456 optimal weight: 10.0000 chunk 688 optimal weight: 30.0000 chunk 633 optimal weight: 20.0000 chunk 548 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 423 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 85782 Z= 0.193 Angle : 0.571 27.181 124338 Z= 0.292 Chirality : 0.038 1.891 15407 Planarity : 0.004 0.062 9104 Dihedral : 23.834 179.897 33286 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 2.65 % Allowed : 21.29 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 5134 helix: 0.62 (0.11), residues: 2047 sheet: -1.16 (0.20), residues: 625 loop : -1.14 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 360 HIS 0.005 0.001 HIS F 81 PHE 0.028 0.001 PHE i 80 TYR 0.018 0.001 TYR L 89 ARG 0.005 0.000 ARG K 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 396 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8847 (p90) cc_final: 0.8561 (p90) REVERT: D 454 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7250 (t80) REVERT: D 459 LEU cc_start: -0.0064 (OUTLIER) cc_final: -0.0445 (tt) REVERT: G 202 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8204 (mm-30) REVERT: M 121 MET cc_start: 0.9011 (ttp) cc_final: 0.8690 (ttp) REVERT: N 31 ARG cc_start: 0.9185 (ttm170) cc_final: 0.8941 (tpp80) REVERT: V 74 MET cc_start: 0.7455 (ppp) cc_final: 0.6118 (ppp) REVERT: W 97 SER cc_start: 0.6578 (p) cc_final: 0.6184 (m) REVERT: W 217 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8273 (p) REVERT: b 136 MET cc_start: 0.8452 (mmm) cc_final: 0.8185 (mmm) REVERT: b 317 ILE cc_start: 0.8259 (pt) cc_final: 0.8002 (mt) REVERT: e 66 LEU cc_start: 0.8390 (mm) cc_final: 0.8101 (mm) REVERT: h 67 ARG cc_start: 0.9586 (ttm-80) cc_final: 0.9300 (ttp80) REVERT: m 311 TRP cc_start: 0.6543 (OUTLIER) cc_final: 0.4477 (m-90) REVERT: n 149 ASN cc_start: 0.8576 (p0) cc_final: 0.8212 (p0) REVERT: n 186 VAL cc_start: 0.4794 (OUTLIER) cc_final: 0.4510 (t) REVERT: v 60 GLN cc_start: 0.8385 (mp10) cc_final: 0.8021 (mp10) REVERT: y 192 VAL cc_start: 0.5546 (OUTLIER) cc_final: 0.5301 (t) outliers start: 121 outliers final: 110 residues processed: 485 average time/residue: 1.6851 time to fit residues: 1334.2100 Evaluate side-chains 506 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 390 time to evaluate : 6.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 72 HIS Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 211 SER Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 384 ASN Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 88 HIS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 100 HIS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 311 TRP Chi-restraints excluded: chain m residue 355 GLU Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain m residue 386 GLU Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 186 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 253 ASP Chi-restraints excluded: chain n residue 389 SER Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain r residue 20 HIS Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 69 GLU Chi-restraints excluded: chain t residue 71 GLU Chi-restraints excluded: chain t residue 151 LEU Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 44 ASP Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 215 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 336 optimal weight: 10.0000 chunk 435 optimal weight: 7.9990 chunk 583 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 505 optimal weight: 30.0000 chunk 80 optimal weight: 40.0000 chunk 152 optimal weight: 40.0000 chunk 549 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 chunk 563 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 overall best weight: 9.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.054139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.046404 restraints weight = 2811816.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.047304 restraints weight = 1384825.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.047718 restraints weight = 879700.136| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 85782 Z= 0.319 Angle : 0.653 27.809 124338 Z= 0.336 Chirality : 0.041 1.848 15407 Planarity : 0.005 0.060 9104 Dihedral : 23.990 178.997 33286 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.57 % Favored : 91.39 % Rotamer: Outliers : 2.60 % Allowed : 21.58 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5134 helix: 0.20 (0.11), residues: 2043 sheet: -1.29 (0.20), residues: 631 loop : -1.43 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP e 32 HIS 0.008 0.002 HIS O 72 PHE 0.021 0.002 PHE i 80 TYR 0.026 0.002 TYR o 89 ARG 0.007 0.001 ARG n 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35243.91 seconds wall clock time: 609 minutes 7.04 seconds (36547.04 seconds total)